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Alpsoy A, Wu XS, Pal S, Klingbeil O, Kumar P, El Demerdash O, Nalbant B, Vakoc CR. IκBζ is a dual-use coactivator of NF-κB and POU transcription factors. Mol Cell 2024; 84:1149-1157.e7. [PMID: 38309274 PMCID: PMC10960667 DOI: 10.1016/j.molcel.2024.01.007] [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: 07/28/2023] [Revised: 12/01/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
OCA-B, OCA-T1, and OCA-T2 belong to a family of coactivators that bind to POU transcription factors (TFs) to regulate gene expression in immune cells. Here, we identify IκBζ (encoded by the NFKBIZ gene) as an additional coactivator of POU TFs. Although originally discovered as an inducible regulator of NF-κB, we show here that IκBζ shares a microhomology with OCA proteins and uses this segment to bind to POU TFs and octamer-motif-containing DNA. Our functional experiments suggest that IκBζ requires its interaction with POU TFs to coactivate immune-related genes. This finding is reinforced by epigenomic analysis of MYD88L265P-mutant lymphoma cells, which revealed colocalization of IκBζ with the POU TF OCT2 and NF-κB:p50 at hundreds of DNA elements harboring octamer and κB motifs. These results suggest that IκBζ is a transcriptional coactivator that can amplify and integrate the output of NF-κB and POU TFs at inducible genes in immune cells.
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Affiliation(s)
- Aktan Alpsoy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Xiaoli S Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sujay Pal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Pramod Kumar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Benan Nalbant
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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2
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Sroka MW, Skopelitis D, Vermunt MW, Preall JB, El Demerdash O, de Almeida LMN, Chang K, Utama R, Gryder B, Caligiuri G, Ren D, Nalbant B, Milazzo JP, Tuveson DA, Dobin A, Hiebert SW, Stengel KR, Mantovani R, Khan J, Kohli RM, Shi J, Blobel GA, Vakoc CR. Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3-FOXO1 in rhabdomyosarcoma. Proc Natl Acad Sci U S A 2023; 120:e2303859120. [PMID: 37639593 PMCID: PMC10483665 DOI: 10.1073/pnas.2303859120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 03/15/2023] [Accepted: 07/11/2023] [Indexed: 08/31/2023] Open
Abstract
Recurrent chromosomal rearrangements found in rhabdomyosarcoma (RMS) produce the PAX3-FOXO1 fusion protein, which is an oncogenic driver and a dependency in this disease. One important function of PAX3-FOXO1 is to arrest myogenic differentiation, which is linked to the ability of RMS cells to gain an unlimited proliferation potential. Here, we developed a phenotypic screening strategy for identifying factors that collaborate with PAX3-FOXO1 to block myo-differentiation in RMS. Unlike most genes evaluated in our screen, we found that loss of any of the three subunits of the Nuclear Factor Y (NF-Y) complex leads to a myo-differentiation phenotype that resembles the effect of inactivating PAX3-FOXO1. While the transcriptomes of NF-Y- and PAX3-FOXO1-deficient RMS cells bear remarkable similarity to one another, we found that these two transcription factors occupy nonoverlapping sites along the genome: NF-Y preferentially occupies promoters, whereas PAX3-FOXO1 primarily binds to distal enhancers. By integrating multiple functional approaches, we map the PAX3 promoter as the point of intersection between these two regulators. We show that NF-Y occupies CCAAT motifs present upstream of PAX3 to function as a transcriptional activator of PAX3-FOXO1 expression in RMS. These findings reveal a critical upstream role of NF-Y in the oncogenic PAX3-FOXO1 pathway, highlighting how a broadly essential transcription factor can perform tumor-specific roles in governing cellular state.
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Affiliation(s)
| | | | - Marit W. Vermunt
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | | | | | | | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Raditya Utama
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Berkley Gryder
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH44106
| | | | - Diqiu Ren
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Benan Nalbant
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | | | | | | | - Scott W. Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232
| | - Kristy R. Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY10461
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133Milano, Italy
| | - Javed Khan
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD20892
| | - Rahul M. Kohli
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA19104
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Gerd A. Blobel
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
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3
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Gryder BE, Wachtel M, Ewert W, Chang K, El Demerdash O, Song Y, Schäfer BW, Vakoc CR, Khan J. Abstract B12: PAX3 translocations co-opt super enhancers and intrinsically disordered fusion partners in rhabdomyosarcoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.pedca19-b12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Chromosomal translocations drive many types of childhood cancer. Fusion-positive rhabdomyosarcoma (FP-RMS) tumors are found most frequently with a fusion between PAX3 and FOXO1, but less frequent translocation partners have been discovered, including INO80D and NCOA1. We hypothesized that all FP-RMS translocations are selecting simultaneously for (1) enhancers active in a myoblast-like epigenome and (2) protein partners with high-levels of intrinsic disorder to give PAX3 enhanced transcriptional strength. Analysis of primary tumors revealed these diverse PAX3 fusions recapitulate a near-identical transcriptome, suggesting uniform underlying molecular mechanisms. ChIP-seq evidence from cell lines and primary tumors suggested that in all FP-RMS tumors, large super-enhancer (SE) elements were present near each chosen translocation partner (distal to FOXO1, INO80D, or NCOA1). Using tools to determine the 3-D folding of chromatin (3C, 4C-seq, and HiChIP), we discovered an extensive network of hijacked FOXO1 enhancers and a SE that physically interact together and with the PAX3 promoter, only in PAX3-FOXO1 positive cells. Furthermore, pooled CRISPR tiling of cis-regulatory elements revealed special dependence on the FOXO1 SE, or certain CTCF boundary elements that facilitate enhancer interactions. ChIP-seq paired to short-term CRISPR experiments shows PAX3-FOXO1 transcription depends on an extended network of related enhancers distal to FOXO1. We find these enhancers are unique to early myoblast stages of differentiation and are bound by myogenic TFs in RMS, suggesting miswiring of normal myogenic enhancer logic. While many SE-driven genes exist in FP-RMS, most are never selected for translocation partners. We found that FOXO1, INO80D, and NCOA1 are all highly disordered proteins, a theme they hold in common despite having no amino acid sequence homology. Initial evidence suggests that PAX3-FOXO1 enables the formation of phase condensates in the nucleus that recruit high-levels of transcriptional machinery such as BRD4. Ongoing work is exploring the mechanistic chemical determinants of these interactions, and how phase condensates are manipulated by drugs that block PAX3-FOXO1’s transcriptional output. Together our studies are illuminating new paradigms for understanding how fusion transcription factors drive cancer.
Citation Format: Berkley E. Gryder, Marco Wachtel, Winston Ewert, Kenneth Chang, Osama El Demerdash, Young Song, Beat W Schäfer, Christopher R. Vakoc, Javed Khan. PAX3 translocations co-opt super enhancers and intrinsically disordered fusion partners in rhabdomyosarcoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B12.
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Affiliation(s)
| | - Marco Wachtel
- 2University Children’s Hospital, Zurich, Switzerland,
| | | | - Kenneth Chang
- 4Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | | | - Young Song
- 1Genetics Branch, NCI, NIH, Bethesda, MD,
| | | | | | - Javed Khan
- 1Genetics Branch, NCI, NIH, Bethesda, MD,
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4
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Gryder BE, Wachtel M, Chang K, El Demerdash O, Aboreden NG, Mohammed W, Ewert W, Pomella S, Rota R, Wei JS, Song Y, Stanton BZ, Schäfer B, Vakoc CR, Khan J. Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage. iScience 2020; 23:101103. [PMID: 32416589 PMCID: PMC7226896 DOI: 10.1016/j.isci.2020.101103] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/31/2020] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
Core regulatory transcription factors (CR TFs) establish enhancers with logical ordering during embryogenesis and development. Here we report that in fusion-positive rhabdomyosarcoma, a cancer of the muscle lineage, the chief oncogene PAX3-FOXO1 is driven by a translocated FOXO1 super enhancer (SE) restricted to a late stage of myogenesis. Using chromatin conformation capture techniques, we demonstrate that the extensive FOXO1 cis-regulatory domain interacts with PAX3. Furthermore, RNA sequencing and chromatin immunoprecipitation sequencing data in tumors bearing rare PAX translocations implicate enhancer miswiring across all fusion-positive tumors. HiChIP of H3K27ac showed connectivity between the FOXO1 SE, additional intra-domain enhancers, and the PAX3 promoter. We show that PAX3-FOXO1 transcription is diminished when this network of enhancers is ablated by CRISPR. Our data reveal a hijacked enhancer network that disrupts the stepwise CR TF logic of normal skeletal muscle development (PAX3 to MYOD to MYOG), replacing it with an "infinite loop" enhancer logic that locks rhabdomyosarcoma in an undifferentiated stage.
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Affiliation(s)
- Berkley E Gryder
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | | | - Kenneth Chang
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Osama El Demerdash
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | | | - Wardah Mohammed
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - Silvia Pomella
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesu' Research Institute, IRCCS, Rome, Italy
| | - Rossella Rota
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesu' Research Institute, IRCCS, Rome, Italy
| | - Jun S Wei
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Young Song
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Benjamin Z Stanton
- Center for Childhood Cancer & Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Beat Schäfer
- University Children's Hospital, Zurich, Switzerland
| | - Christopher R Vakoc
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Javed Khan
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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5
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Tarumoto Y, Lu B, Somerville TDD, Huang YH, Milazzo JP, Wu XS, Klingbeil O, El Demerdash O, Shi J, Vakoc CR. LKB1, Salt-Inducible Kinases, and MEF2C Are Linked Dependencies in Acute Myeloid Leukemia. Mol Cell 2018. [PMID: 29526696 DOI: 10.1016/j.molcel.2018.02.011] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The lineage-specific transcription factor (TF) MEF2C is often deregulated in leukemia. However, strategies to target this TF have yet to be identified. Here, we used a domain-focused CRISPR screen to reveal an essential role for LKB1 and its Salt-Inducible Kinase effectors (SIK3, in a partially redundant manner with SIK2) to maintain MEF2C function in acute myeloid leukemia (AML). A key phosphorylation substrate of SIK3 in this context is HDAC4, a repressive cofactor of MEF2C. Consequently, targeting of LKB1 or SIK3 diminishes histone acetylation at MEF2C-bound enhancers and deprives leukemia cells of the output of this essential TF. We also found that MEF2C-dependent leukemias are sensitive to on-target chemical inhibition of SIK activity. This study reveals a chemical strategy to block MEF2C function in AML, highlighting how an oncogenic TF can be disabled by targeting of upstream kinases.
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Affiliation(s)
- Yusuke Tarumoto
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bin Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Yu-Han Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joseph P Milazzo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Xiaoli S Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Genetics Program, Stony Brook University, Stony Brook, NY 11794, USA
| | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Junwei Shi
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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6
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Diermeier SD, Chang KC, Freier SM, Song J, El Demerdash O, Krasnitz A, Rigo F, Bennett CF, Spector DL. Mammary Tumor-Associated RNAs Impact Tumor Cell Proliferation, Invasion, and Migration. Cell Rep 2017; 17:261-274. [PMID: 27681436 DOI: 10.1016/j.celrep.2016.08.081] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 08/05/2016] [Accepted: 08/23/2016] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) represent the largest and most diverse class of non-coding RNAs, comprising almost 16,000 currently annotated transcripts in human and 10,000 in mouse. Here, we investigated the role of lncRNAs in mammary tumors by performing RNA-seq on tumor sections and organoids derived from MMTV-PyMT and MMTV-Neu-NDL mice. We identified several hundred lncRNAs that were overexpressed compared to normal mammary epithelium. Among these potentially oncogenic lncRNAs we prioritized a subset as Mammary Tumor Associated RNAs (MaTARs) and determined their human counterparts, hMaTARs. To functionally validate the role of MaTARs, we performed antisense knockdown and observed reduced cell proliferation, invasion, and/or organoid branching in a cancer-specific context. Assessing the expression of hMaTARs in human breast tumors revealed that 19 hMaTARs are significantly upregulated and many of these correlate with breast cancer subtype and/or hormone receptor status, indicating potential clinical relevance.
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Affiliation(s)
| | - Kung-Chi Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Junyan Song
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Alexander Krasnitz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | | | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY 11794, USA.
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7
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Zhou X, Battistoni G, El Demerdash O, Gurtowski J, Wunderer J, Falciatori I, Ladurner P, Schatz MC, Hannon GJ, Wasik KA. Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano. RNA 2015; 21:1885-97. [PMID: 26323280 PMCID: PMC4604429 DOI: 10.1261/rna.052456.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 06/29/2015] [Indexed: 06/04/2023]
Abstract
PIWI proteins and piRNA pathways are essential for transposon silencing and some aspects of gene regulation during animal germline development. In contrast to most animal species, some flatworms also express PIWIs and piRNAs in somatic stem cells, where they are required for tissue renewal and regeneration. Here, we have identified and characterized piRNAs and PIWI proteins in the emerging model flatworm Macrostomum lignano. We found that M. lignano encodes at least three PIWI proteins. One of these, Macpiwi1, acts as a key component of the canonical piRNA pathway in the germline and in somatic stem cells. Knockdown of Macpiwi1 dramatically reduces piRNA levels, derepresses transposons, and severely impacts stem cell maintenance. Knockdown of the piRNA biogenesis factor Macvasa caused an even greater reduction in piRNA levels with a corresponding increase in transposons. Yet, in Macvasa knockdown animals, we detected no major impact on stem cell self-renewal. These results may suggest stem cell maintenance functions of PIWI proteins in flatworms that are distinguishable from their impact on transposons and that might function independently of what are considered canonical piRNA populations.
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Affiliation(s)
- Xin Zhou
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA Molecular and Cellular Biology Graduate Program, Stony Brook University, Stony Brook, New York 11794, USA
| | - Giorgia Battistoni
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Osama El Demerdash
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - James Gurtowski
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Julia Wunderer
- University of Innsbruck, Institute of Zoology and CMBI, A-6020 Innsbruck, Austria
| | - Ilaria Falciatori
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Peter Ladurner
- University of Innsbruck, Institute of Zoology and CMBI, A-6020 Innsbruck, Austria
| | - Michael C Schatz
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Gregory J Hannon
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Kaja A Wasik
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
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8
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Wasik K, Gurtowski J, Zhou X, Ramos OM, Delás MJ, Battistoni G, El Demerdash O, Falciatori I, Vizoso DB, Smith AD, Ladurner P, Schärer L, McCombie WR, Hannon GJ, Schatz M. Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc Natl Acad Sci U S A 2015; 112:12462-7. [PMID: 26392545 PMCID: PMC4603488 DOI: 10.1073/pnas.1516718112] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [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] [Indexed: 01/08/2023] Open
Abstract
The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cell-fate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of M. lignano and an accompanying characterization of its transcriptome. The genome structure of M. lignano is remarkably complex, with ∼75% of its sequence being comprised of simple repeats and transposon sequences. This has made high-quality assembly from Illumina reads alone impossible (N50=222 bp). We therefore generated 130× coverage by long sequencing reads from the Pacific Biosciences platform to create a substantially improved assembly with an N50 of 64 Kbp. We complemented the reference genome with an assembled and annotated transcriptome, and used both of these datasets in combination to probe gene-expression patterns during regeneration, examining pathways important to stem cell function.
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Affiliation(s)
- Kaja Wasik
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - James Gurtowski
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Xin Zhou
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Molecular and Cellular Biology Graduate Program, Stony Brook University, NY 11794
| | - Olivia Mendivil Ramos
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - M Joaquina Delás
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Giorgia Battistoni
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Osama El Demerdash
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Ilaria Falciatori
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Dita B Vizoso
- Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Andrew D Smith
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
| | - Peter Ladurner
- Department of Evolutionary Biology, Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Lukas Schärer
- Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - W Richard McCombie
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom;
| | - Michael Schatz
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
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9
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Knott SR, Maceli A, Erard N, Chang K, Marran K, Zhou X, Gordon A, Demerdash OE, Wagenblast E, Kim S, Fellmann C, Hannon GJ. A computational algorithm to predict shRNA potency. Mol Cell 2014; 56:796-807. [PMID: 25435137 PMCID: PMC4272634 DOI: 10.1016/j.molcel.2014.10.025] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [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: 04/03/2014] [Revised: 09/11/2014] [Accepted: 10/23/2014] [Indexed: 12/16/2022]
Abstract
The strength of conclusions drawn from RNAi-based studies is heavily influenced by the quality of tools used to elicit knockdown. Prior studies have developed algorithms to design siRNAs. However, to date, no established method has emerged to identify effective shRNAs, which have lower intracellular abundance than transfected siRNAs and undergo additional processing steps. We recently developed a multiplexed assay for identifying potent shRNAs and used this method to generate ∼250,000 shRNA efficacy data points. Using these data, we developed shERWOOD, an algorithm capable of predicting, for any shRNA, the likelihood that it will elicit potent target knockdown. Combined with additional shRNA design strategies, shERWOOD allows the ab initio identification of potent shRNAs that specifically target the majority of each gene's multiple transcripts. We validated the performance of our shRNA designs using several orthogonal strategies and constructed genome-wide collections of shRNAs for humans and mice based on our approach.
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Affiliation(s)
- Simon R.V. Knott
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Ashley Maceli
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Nicolas Erard
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Kenneth Chang
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Krista Marran
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Xin Zhou
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Assaf Gordon
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Osama El Demerdash
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Elvin Wagenblast
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Sun Kim
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Christof Fellmann
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Gregory J. Hannon
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
- Cancer Research UK Cambridge Insitute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB20RE, UK
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