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Sasidharan R, Brokate L, Eilers EJ, Müller C. Chemodiversity in flowers of Tanacetum vulgare has consequences on a florivorous beetle. Plant Biol (Stuttg) 2023; 25:1071-1082. [PMID: 37703504 DOI: 10.1111/plb.13576] [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] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/18/2023] [Indexed: 09/15/2023]
Abstract
The chemical composition of plant individuals can vary, leading to high intraspecific chemodiversity. Diversity of floral chemistry may impact the responses of flower-feeding insects. Tanacetum vulgare plants vary significantly in their leaf terpenoid composition, forming distinct chemotypes. We investigated the composition of terpenoids and nutrients of flower heads and pollen in plants belonging to three chemotypes - dominated either by β-thujone (BThu), artemisia ketone (Keto) or a mixture of (Z)-myroxide, santolina triene, and artemisyl acetate (Myrox) - using different analytical platforms. We tested the effects of these differences on preferences, weight gain and performance of adults of the shining flower beetle, Olibrus aeneus. The terpenoid composition and diversity of flower heads and pollen significantly differed among individuals belonging to the above chemotypes, while total concentrations of pollen terpenoids, sugars, amino acids, and lipids did not differ. Beetles preferred BThu over the Myrox chemotype in both olfactory and contact choice assays, while the Keto chemotype was marginally repellent according to olfactory assays. The beetles gained the least weight within 48 h and their initial mortality was highest when feeding exclusively on floral tissues of the Myrox chemotype. Short-term weight gain and long-term performance were highest when feeding on the BThu chemotype. In conclusion, the beetles showed chemotype-specific responses towards different T. vulgare chemotypes, which may be attributed to the terpenoid composition in flower heads and pollen rather than to differences in nutrient profiles. Both richness and overall diversity are important factors when determining chemodiversity of individual plants and their consequences on interacting insects.
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Affiliation(s)
- R Sasidharan
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
| | - L Brokate
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
| | - E J Eilers
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
- CTL GmbH Bielefeld, Bielefeld, Germany
| | - C Müller
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
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2
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Kumar P, Zhang N, Lee J, Cheng H, Kurtz K, Conneely SE, Sasidharan R, Rau RE, Pati D. Cohesin Subunit RAD21 Regulates the Differentiation and Self-Renewal of Hematopoietic Stem and Progenitor Cells. Stem Cells 2023; 41:971-985. [PMID: 37534584 DOI: 10.1093/stmcls/sxad058] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/21/2023] [Indexed: 08/04/2023]
Abstract
Recent studies suggest that chromosomal cohesin complex proteins are important in regulating hematopoiesis and may contribute to myeloid malignancies. To investigate the effects of perturbing the cohesin subunit protein RAD21 on normal hematopoiesis, we used conditional knockout (cKO) mouse models. While cohesin is vital for hematopoietic stem cell (HSC) function, Rad21 haploinsufficiency (Rad21Δ/+) led to distinct hematopoietic phenotypes. Our findings revealed that Rad21Δ/+ cells exhibited decreased hematopoietic reconstitution in competitive bone marrow transplantation assays. This reduction in peripheral blood chimerism was specifically observed in the lymphoid compartment, while the chimerism in the myeloid compartment remained unaffected. Rad21 haploinsufficiency also resulted in changes in the hematopoietic stem and progenitor cells (HSPC) and myeloid progenitor compartments, with a significant accumulation of granulocyte-macrophage progenitors in the bone marrow. We observed differential gene expression in Rad21Δ/+ LSK (Lin- Sca1-Kit+) cells, including genes required for HSPC function and differentiation, such as Setdb1, Hmga2, Ncor1, and Myb. In addition, we observed a notable decrease in the expression of genes related to the interferon response and a significant reduction in the expression of genes involved in the IL2-STAT5 signaling pathways. Our studies suggest that RAD21 protein and level of its post-translational modifications in the bone marrow cells may play a potential role in hematopoiesis. Overall, Rad21 haploinsufficiency impairs hematopoietic differentiation and increases HSC self-renewal.
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Affiliation(s)
- Praveen Kumar
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Nenggang Zhang
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - John Lee
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Haizi Cheng
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Kristen Kurtz
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Shannon E Conneely
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Rachel E Rau
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Debananda Pati
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
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Hultmark S, Baudet A, Schmiderer L, Prabhala P, Palma-Tortosa S, Sandén C, Fioretos T, Sasidharan R, Larsson C, Lehmann S, Juliusson G, Ek F, Magnusson M. Combinatorial molecule screening identified a novel diterpene and the BET inhibitor CPI-203 as differentiation inducers of primary acute myeloid leukemia cells. Haematologica 2021; 106:2566-2577. [PMID: 32855276 PMCID: PMC8485661 DOI: 10.3324/haematol.2020.249177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
Combination treatment has proven effective for patients with acute promyelocytic leukemia, exemplifying the importance of therapy targeting multiple components of oncogenic regulation for a successful outcome. However, recent studies have shown that the mutational complexity of acute myeloid leukemia (AML) precludes the translation of molecular targeting into clinical success. Here, as a complement to genetic profiling, we used unbiased, combinatorial in vitro drug screening to identify pathways that drive AML and to develop personalized combinatorial treatments. First, we screened 513 natural compounds on primary AML cells and identified a novel diterpene (H4) that preferentially induced differentiation of FLT3 wild-type AML, while FLT3-ITD/mutations conferred resistance. The samples responding to H4, displayed increased expression of myeloid markers, a clear decrease in the nuclear-cytoplasmic ratio and the potential of re-activation of the monocytic transcriptional program reducing leukemia propagation in vivo. By combinatorial screening using H4 and molecules with defined targets, we demonstrated that H4 induces differentiation by the activation of the protein kinase C (PKC) signaling pathway, and in line with this, activates PKC phosphorylation and translocation of PKC to the cell membrane. Furthermore, the combinatorial screening identified a bromo- and extra-terminal domain (BET) inhibitor that could further improve H4-dependent leukemic differentiation in FLT3 wild-type monocytic AML. These findings illustrate the value of an unbiased, multiplex screening platform for developing combinatorial therapeutic approaches for AML.
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Affiliation(s)
- Simon Hultmark
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Sweden
| | - Aurélie Baudet
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Sweden
| | - Ludwig Schmiderer
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Sweden
| | - Pavan Prabhala
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Sara Palma-Tortosa
- Laboratory of Stem Cells and Restorative Neurology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Carl Sandén
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | | | - Christer Larsson
- Division of Translational Cancer Research, Lund University, Lund, Sweden
| | - Sören Lehmann
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Gunnar Juliusson
- Department of Hematology, Skane University Hospital, Lund, Sweden
| | - Fredrik Ek
- Chemical Biology and Therapeutics, Lund University, Lund, Sweden
| | - Mattias Magnusson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Sweden
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Sasidharan R, Bhattacharyya T, H Lal V, Mallick I, ArunSingh M, Chakraborty S, Basu Achari R, Chatterjee S. PO-1233 Real world results of CTRT in Ca esophagus: Can SCOPE-1 results be replicated outside trial setting? Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)07684-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kumar P, Cheng H, Paudyal S, Nakamura LV, Zhang N, Li JT, Sasidharan R, Jeong M, Pati D. Haploinsufficiency of cohesin protease, Separase, promotes regeneration of hematopoietic stem cells in mice. Stem Cells 2020; 38:1624-1636. [PMID: 32997844 DOI: 10.1002/stem.3280] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/23/2020] [Accepted: 08/31/2020] [Indexed: 11/09/2022]
Abstract
Cohesin recently emerged as a new regulator of hematopoiesis and leukemia. In addition to cohesin, whether proteins that regulate cohesin's function have any direct role in hematopoiesis and hematologic diseases have not been fully examined. Separase, encoded by the ESPL1 gene, is an important regulator of cohesin's function. Canonically, protease activity of Separase resolves sister chromatid cohesion by cleaving cohesin subunit-Rad21 at the onset of anaphase. Using a Separase haploinsufficient mouse model, we have uncovered a novel role of Separase in hematopoiesis. We report that partial disruption of Separase distinctly alters the functional characteristics of hematopoietic stem/progenitor cells (HSPCs). Although analyses of peripheral blood and bone marrow of Espl1+/Hyp mice broadly displayed unperturbed hematopoietic parameters during normal hematopoiesis, further probing of the composition of early hematopoietic cells in Espl1+/Hyp bone marrow revealed a mild reduction in the frequencies of the Lin- Sca1+ Kit- (LSK) or LSK CD48+ CD150- multipotent hematopoietic progenitors population without a significant change in either long-term or short-term hematopoietic stem cells (HSCs) subsets at steady state. Surprisingly, however, we found that Separase haploinsufficiency promotes regeneration activity of HSCs in serial in vivo repopulation assays. In vitro colony formation assays also revealed an enhanced serial replating capacity of hematopoietic progenitors isolated from Espl1+/Hyp mice. Microarray analysis of differentially expressed genes showed that Separase haploinsufficiency in HSCs (SP-KSL) leads to enrichment of gene signatures that are upregulated in HSCs compared to committed progenitors and mature cells. Taken together, our findings demonstrate a key role of Separase in promoting hematopoietic regeneration of HSCs.
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Affiliation(s)
- Praveen Kumar
- Texas Childrens Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Haizi Cheng
- Texas Childrens Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Samridhdi Paudyal
- Texas Childrens Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Lanelle V Nakamura
- Texas Childrens Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Nenggang Zhang
- Texas Childrens Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Jessica T Li
- Texas Childrens Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Mira Jeong
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Debananda Pati
- Texas Childrens Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
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Morales A, Teapal J, Ammerlaan JMH, Yin X, Evers JB, Anten NPR, Sasidharan R, van Zanten M. A high throughput method for quantifying number and size distribution of Arabidopsis seeds using large particle flow cytometry. Plant Methods 2020; 16:27. [PMID: 32158493 PMCID: PMC7053093 DOI: 10.1186/s13007-020-00572-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/20/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Seed size and number are important plant traits from an ecological and horticultural/agronomic perspective. However, in small-seeded species such as Arabidopsis thaliana, research on seed size and number is limited by the absence of suitable high throughput phenotyping methods. RESULTS We report on the development of a high throughput method for counting seeds and measuring individual seed sizes. The method uses a large-particle flow cytometer to count individual seeds and sort them according to size, allowing an average of 12,000 seeds/hour to be processed. To achieve this high throughput, post harvested seeds are first separated from remaining plant material (dust and chaff) using a rapid sedimentation-based method. Then, classification algorithms are used to refine the separation process in silico. Accurate identification of all seeds in the samples was achieved, with relative errors below 2%. CONCLUSION The tests performed reveal that there is no single classification algorithm that performs best for all samples, so the recommended strategy is to train and use multiple algorithms and use the median predictions of seed size and number across all algorithms. To facilitate the use of this method, an R package (SeedSorter) that implements the methodology has been developed and made freely available. The method was validated with seed samples from several natural accessions of Arabidopsis thaliana, but our analysis pipeline is applicable to any species with seed sizes smaller than 1.5 mm.
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Affiliation(s)
- Alejandro Morales
- Centre for Crop Systems Analysis, Plant Sciences Group, Wageningen University & Research, Wageningen, The Netherlands
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - J. Teapal
- Developmental Biology, Institute of Biodynamics and Biocomplexity, Utrecht University, Utrecht, The Netherlands
| | - J. M. H. Ammerlaan
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - X. Yin
- Centre for Crop Systems Analysis, Plant Sciences Group, Wageningen University & Research, Wageningen, The Netherlands
| | - J. B. Evers
- Centre for Crop Systems Analysis, Plant Sciences Group, Wageningen University & Research, Wageningen, The Netherlands
| | - N. P. R. Anten
- Centre for Crop Systems Analysis, Plant Sciences Group, Wageningen University & Research, Wageningen, The Netherlands
| | - R. Sasidharan
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - M. van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
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Wright AA, Sasidharan R, Koski L, Rodriguez-Carres M, Peterson DG, Nandula VK, Ray JD, Bond JA, Shaw DR. Transcriptomic changes in Echinochloa colona in response to treatment with the herbicide imazamox. Planta 2018; 247:369-379. [PMID: 29022094 DOI: 10.1007/s00425-017-2784-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023]
Abstract
Presented here is the first Echinochloa colona leaf transcriptome. Analysis of gene expression before and after herbicide treatment reveals that E. colona mounts a stress response upon exposure to herbicide. Herbicides are the most frequently used means of controlling weeds. For many herbicides, the target site is known; however, it is considerably less clear how plant gene expression changes in response to herbicide exposure. In this study, changes in gene expression in response to herbicide exposure in imazamox-sensitive (S) and- resistant (R) junglerice (Echinochloa colona L.) biotypes was examined. As no reference genome is available for this weed, a reference leaf transcriptome was generated. Messenger RNA was isolated from imazamox-treated- and untreated R and S plants and the resulting cDNA libraries were sequenced on an Illumina HiSeq2000. The transcriptome was assembled, annotated, and differential gene expression analysis was performed to identify transcripts that were upregulated or downregulated in response to herbicide exposure for both biotypes. Differentially expressed transcripts included transcription factors, protein-modifying enzymes, and enzymes involved in metabolism and signaling. A literature search revealed that members of the families represented in this analysis were known to be involved in abiotic stress response in other plants, suggesting that imazamox exposure induced a stress response. A time course study examining a subset of transcripts showed that expression peaked within 4-12 h and then returned to untreated levels within 48 h of exposure. Testing of plants from two additional biotypes showed a similar change in gene expression 4 h after herbicide exposure compared to the resistant and sensitive biotypes. This study shows that within 48 h junglerice mounts a stress response to imazamox exposure.
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Affiliation(s)
- Alice A Wright
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, 39762, USA.
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, 99350, USA.
| | - Rajkumar Sasidharan
- BASF, Research Triangle Park, NC, 27709, USA
- Solvuu, Inc, New York, NY, 10017, USA
| | - Liisa Koski
- BASF, Research Triangle Park, NC, 27709, USA
| | | | - Daniel G Peterson
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Vijay K Nandula
- Crop Production Systems Research Unit, USDA-ARS, Stoneville, MS, 38776, USA
| | - Jeffery D Ray
- Crop Genetics Research Unit, USDA-ARS, Stoneville, MS, 38776, USA
| | - Jason A Bond
- Department of Plant and Soil Sciences, Mississippi State University, Stoneville, MS, 38776, USA
| | - David R Shaw
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, 39762, USA
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Karim S, Ding K, Bradbury P, Ellis P, Mittman N, Xiaoqun Sun X, Millward M, Liu G, Sun S, Stockler M, Cohen V, Blais N, Sangha R, Boyer M, Sasidharan R, Lee C, Shepherd F, Goss G, Seymour L, Leighl N. Costs of dacomitinib versus placebo in pretreated unselected patients (pts) with advanced NSCLC: CCTG BR.26. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx375.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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9
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Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo DCE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SME, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SCE, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk ADJ, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZN, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJE, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biol 2016; 17:184. [PMID: 27604469 PMCID: PMC5015320 DOI: 10.1186/s13059-016-1037-6] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [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: 10/26/2015] [Accepted: 08/04/2016] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. RESULTS We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. CONCLUSIONS The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.
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Affiliation(s)
- Yuxiang Jiang
- Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA
| | | | - Wyatt T Clark
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Asma R Bankapur
- Department of Microbiology, Miami University, Oxford, OH, USA
| | | | | | - Christopher S Funk
- Computational Bioscience Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Indika Kahanda
- Department of Computer Science, Colorado State University, Fort Collins, CO, USA
| | - Karin M Verspoor
- Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria, Australia
- Health and Biomedical Informatics Centre, University of Melbourne, Parkville, Victoria, Australia
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, CO, USA
| | | | - Duncan Penfold-Brown
- Social Media and Political Participation Lab, New York University, New York, NY, USA
- CY Data Science, New York, NY, USA
| | - Dennis Shasha
- Department of Computer Science, New York University, New York, NY, USA
| | - Noah Youngs
- CY Data Science, New York, NY, USA
- Department of Computer Science, New York University, New York, NY, USA
- Simons Center for Data Analysis, New York, NY, USA
| | - Richard Bonneau
- Department of Computer Science, New York University, New York, NY, USA
- Simons Center for Data Analysis, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Alexandra Lin
- Department of Electrical Engineering and Computer Sciences, University of California Berkeley, Berkeley, CA, USA
| | - Sayed M E Sahraeian
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | | | - Giuseppe Profiti
- Biocomputing Group, BiGeA, University of Bologna, Bologna, Italy
| | - Rita Casadio
- Biocomputing Group, BiGeA, University of Bologna, Bologna, Italy
| | - Renzhi Cao
- Computer Science Department, University of Missouri, Columbia, MO, USA
| | - Zhaolong Zhong
- Computer Science Department, University of Missouri, Columbia, MO, USA
| | - Jianlin Cheng
- Computer Science Department, University of Missouri, Columbia, MO, USA
| | - Adrian Altenhoff
- ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Nives Skunca
- ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Christophe Dessimoz
- Bioinformatics Group, Department of Computer Science, University College London, London, UK
- University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tunca Dogan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Kai Hakala
- Department of Information Technology, University of Turku, Turku, Finland
- University of Turku Graduate School, University of Turku, Turku, Finland
| | - Suwisa Kaewphan
- Department of Information Technology, University of Turku, Turku, Finland
- University of Turku Graduate School, University of Turku, Turku, Finland
- Turku Centre for Computer Science, Turku, Finland
| | - Farrokh Mehryary
- Department of Information Technology, University of Turku, Turku, Finland
- University of Turku Graduate School, University of Turku, Turku, Finland
| | - Tapio Salakoski
- Department of Information Technology, University of Turku, Turku, Finland
- Turku Centre for Computer Science, Turku, Finland
| | - Filip Ginter
- Department of Information Technology, University of Turku, Turku, Finland
| | - Hai Fang
- University of Bristol, Bristol, UK
| | | | | | | | - Petri Törönen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Patrik Koskinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Liisa Holm
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Biological and Environmental Sciences, Universitity of Helsinki, Helsinki, Finland
| | - Ching-Tai Chen
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Wen-Lian Hsu
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Kevin Bryson
- Bioinformatics Group, Department of Computer Science, University College London, London, UK
| | - Domenico Cozzetto
- Bioinformatics Group, Department of Computer Science, University College London, London, UK
| | - Federico Minneci
- Bioinformatics Group, Department of Computer Science, University College London, London, UK
| | - David T Jones
- Bioinformatics Group, Department of Computer Science, University College London, London, UK
| | - Samuel Chapman
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA
| | - Dukka Bkc
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA
| | - Ishita K Khan
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Dan Ofer
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nadav Rappoport
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amos Stern
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Elena Cibrian-Uhalte
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Paul Denny
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, UK
| | - Rebecca E Foulger
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, UK
| | - Reija Hieta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Duncan Legge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Ruth C Lovering
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, UK
| | - Michele Magrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Anna N Melidoni
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, UK
| | | | - Klemens Pichler
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Aleksandra Shypitsyna
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Biao Li
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Pooya Zakeri
- Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, Leuven, Belgium
- iMinds Department Medical Information Technologies, Leuven, Belgium
| | - Sarah ElShal
- Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, Leuven, Belgium
- iMinds Department Medical Information Technologies, Leuven, Belgium
| | - Léon-Charles Tranchevent
- Inserm UMR-S1052, CNRS UMR5286, Cancer Research Centre of Lyon, Lyon, France
- Université de Lyon 1, Villeurbanne, France
- Centre Léon Bérard, Lyon, France
| | - Sayoni Das
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Natalie L Dawson
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - David Lee
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Jonathan G Lees
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, University College London, London, UK
| | | | | | - Alfonso E Romero
- Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, UK
| | - Rajkumar Sasidharan
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Haixuan Yang
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
| | - Alberto Paccanaro
- Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, UK
| | - Jesse Gillis
- Stanley Institute for Cognitive Genomics Cold Spring Harbor Laboratory, New York, NY, USA
| | | | - Paul Pavlidis
- Department of Psychiatry and Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Shou Feng
- Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA
| | - Juan M Cejuela
- Department for Bioinformatics and Computational Biology-I12, Technische Universität München, Garching, Germany
| | - Tatyana Goldberg
- Department for Bioinformatics and Computational Biology-I12, Technische Universität München, Garching, Germany
| | - Tobias Hamp
- Department for Bioinformatics and Computational Biology-I12, Technische Universität München, Garching, Germany
| | - Lothar Richter
- Department for Bioinformatics and Computational Biology-I12, Technische Universität München, Garching, Germany
| | - Asaf Salamov
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Toni Gabaldon
- Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Marina Marcet-Houben
- Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Fran Supek
- Universitat Pompeu Fabra, Barcelona, Spain
- Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
| | - Qingtian Gong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Science, Fudan University, Shanghai, China
- Children's Hospital of Fudan University, Shanghai, China
| | - Wei Ning
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Science, Fudan University, Shanghai, China
- Children's Hospital of Fudan University, Shanghai, China
| | - Yuanpeng Zhou
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Science, Fudan University, Shanghai, China
- Children's Hospital of Fudan University, Shanghai, China
| | - Weidong Tian
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Science, Fudan University, Shanghai, China
- Children's Hospital of Fudan University, Shanghai, China
| | - Marco Falda
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Paolo Fontana
- Research and Innovation Center, Edmund Mach Foundation, San Michele all'Adige, Italy
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Carlo Ferrari
- Department of Information Engineering, University of Padua, Padova, Italy
| | - Manuel Giollo
- Department of Information Engineering, University of Padua, Padova, Italy
- Department of Biomedical Sciences, University of Padua, Padova, Italy
| | - Damiano Piovesan
- Department of Information Engineering, University of Padua, Padova, Italy
| | - Silvio C E Tosatto
- Department of Information Engineering, University of Padua, Padova, Italy
| | - Angela Del Pozo
- Instituto De Genetica Medica y Molecular, Hospital Universitario de La Paz, Madrid, Spain
| | - José M Fernández
- Spanish National Bioinformatics Institute, Spanish National Cancer Research Institute, Madrid, Spain
| | - Paolo Maietta
- Structural and Computational Biology Programme, Spanish National Cancer Research Institute, Madrid, Spain
| | - Alfonso Valencia
- Structural and Computational Biology Programme, Spanish National Cancer Research Institute, Madrid, Spain
| | - Michael L Tress
- Structural and Computational Biology Programme, Spanish National Cancer Research Institute, Madrid, Spain
| | - Alfredo Benso
- Control and Computer Engineering Department, Politecnico di Torino, Torino, Italy
| | - Stefano Di Carlo
- Control and Computer Engineering Department, Politecnico di Torino, Torino, Italy
| | - Gianfranco Politano
- Control and Computer Engineering Department, Politecnico di Torino, Torino, Italy
| | - Alessandro Savino
- Control and Computer Engineering Department, Politecnico di Torino, Torino, Italy
| | - Hafeez Ur Rehman
- National University of Computer & Emerging Sciences, Islamabad, Pakistan
| | - Matteo Re
- Anacleto Lab, Dipartimento di informatica, Università degli Studi di Milano, Milan, Italy
| | - Marco Mesiti
- Anacleto Lab, Dipartimento di informatica, Università degli Studi di Milano, Milan, Italy
| | - Giorgio Valentini
- Anacleto Lab, Dipartimento di informatica, Università degli Studi di Milano, Milan, Italy
| | - Joachim W Bargsten
- Applied Bioinformatics, Bioscience, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Aalt D J van Dijk
- Applied Bioinformatics, Bioscience, Wageningen University and Research Centre, Wageningen, Netherlands
- Biometris, Wageningen University, Wageningen, Netherlands
| | - Branislava Gemovic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, Belgrade, Serbia
| | - Sanja Glisic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, Belgrade, Serbia
| | - Vladmir Perovic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, Belgrade, Serbia
| | - Veljko Veljkovic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, Belgrade, Serbia
| | - Nevena Veljkovic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, Belgrade, Serbia
| | | | - Ricardo Z N Vencio
- Department of Computing and Mathematics FFCLRP-USP, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Malvika Sharan
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lakesh Kansakar
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA
| | - Shanshan Zhang
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA
| | - Slobodan Vucetic
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA
| | - Zheng Wang
- University of Southern Mississippi, Hattiesburg, MS, USA
| | - Michael J E Sternberg
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, UK
| | - Mark N Wass
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Rachael P Huntley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Maria J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Peter N Robinson
- Institut für Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Yves Moreau
- Department of Electrical Engineering ESAT-SCD and IBBT-KU Leuven Future Health Department, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Patricia C Babbitt
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, CA, USA
| | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Michal Linial
- Department of Chemical Biology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Christine A Orengo
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Burkhard Rost
- Department for Bioinformatics and Computational Biology-I12, Technische Universität München, Garching, Germany
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Iddo Friedberg
- Department of Microbiology, Miami University, Oxford, OH, USA.
- Department of Computer Science, Miami University, Oxford, OH, USA.
| | - Predrag Radivojac
- Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA.
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10
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Dou DR, Calvanese V, Sierra MI, Nguyen AT, Minasian A, Saarikoski P, Sasidharan R, Ramirez CM, Zack JA, Crooks GM, Galic Z, Mikkola HKA. Medial HOXA genes demarcate haematopoietic stem cell fate during human development. Nat Cell Biol 2016; 18:595-606. [PMID: 27183470 PMCID: PMC4981340 DOI: 10.1038/ncb3354] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [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: 12/22/2014] [Accepted: 04/08/2016] [Indexed: 12/18/2022]
Abstract
Pluripotent stem cells (PSC) may provide a potential source of haematopoietic stem/progenitor cells (HSPCs) for transplantation; however, unknown molecular barriers prevent the self-renewal of PSC-HSPCs. Using two-step differentiation, human embryonic stem cells (hESCs) differentiated in vitro into multipotent haematopoietic cells that had CD34+CD38−/loCD90+CD45+GPI-80+ foetal liver (FL) HSC immunophenotype, but displayed poor expansion potential and engraftment ability. Transcriptome analysis of immunophenotypic hESC-HSPCs revealed that, despite their molecular resemblance to FL-HSPCs, medial HOXA genes remained suppressed. Knockdown of HOXA7 disrupted FL-HSPC function and caused transcriptome dysregulation that resembled hESC-derived progenitors. Overexpression of medial HOXA genes prolonged FL-HSPC maintenance but was insufficient to confer self-renewal to hESC-HSPCs. Stimulation of retinoic acid signalling during endothelial-to-haematopoietic transition induced the HOXA cluster and other HSC/definitive haemogenic endothelium genes, and prolonged HSPC maintenance in culture. Thus, retinoic acid signalling-induced medial HOXA gene expression marks the establishment of the definitive HSC fate and controls HSC identity and function.
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Affiliation(s)
- Diana R Dou
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Vincenzo Calvanese
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Maria I Sierra
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Andrew T Nguyen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Arazin Minasian
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Pamela Saarikoski
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Rajkumar Sasidharan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Christina M Ramirez
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Jerome A Zack
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, USA.,Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, Los Angeles, California 90095, USA.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Gay M Crooks
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, USA.,Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Zoran Galic
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, USA.,Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Hanna K A Mikkola
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
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11
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Dou DR, Calvanese V, Sierra MI, Sasidharan R, Zack JA, Crooks GM, Galic Z, Mikkola H. Medial HOXA gene expression is required for establishing “stemness” in human HSCs. Exp Hematol 2015. [DOI: 10.1016/j.exphem.2015.06.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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12
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Org T, Duan D, Ferrari R, Montel-Hagen A, Van Handel B, Kerényi MA, Sasidharan R, Rubbi L, Fujiwara Y, Pellegrini M, Orkin SH, Kurdistani SK, Mikkola HK. Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence. EMBO J 2015; 34:759-77. [PMID: 25564442 PMCID: PMC4369313 DOI: 10.15252/embj.201490542] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [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] [Indexed: 12/19/2022] Open
Abstract
Scl/Tal1 confers hemogenic competence and prevents ectopic cardiomyogenesis in embryonic endothelium by unknown mechanisms. We discovered that Scl binds to hematopoietic and cardiac enhancers that become epigenetically primed in multipotent cardiovascular mesoderm, to regulate the divergence of hematopoietic and cardiac lineages. Scl does not act as a pioneer factor but rather exploits a pre-established epigenetic landscape. As the blood lineage emerges, Scl binding and active epigenetic modifications are sustained in hematopoietic enhancers, whereas cardiac enhancers are decommissioned by removal of active epigenetic marks. Our data suggest that, rather than recruiting corepressors to enhancers, Scl prevents ectopic cardiogenesis by occupying enhancers that cardiac factors, such as Gata4 and Hand1, use for gene activation. Although hematopoietic Gata factors bind with Scl to both activated and repressed genes, they are dispensable for cardiac repression, but necessary for activating genes that enable hematopoietic stem/progenitor cell development. These results suggest that a unique subset of enhancers in lineage-specific genes that are accessible for regulators of opposing fates during the time of the fate decision provide a platform where the divergence of mutually exclusive fates is orchestrated.
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Affiliation(s)
- Tõnis Org
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Dan Duan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Roberto Ferrari
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
| | - Amelie Montel-Hagen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Ben Van Handel
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Marc A Kerényi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute Harvard Stem Cell Institute Harvard Medical School, Boston, MA, USA
| | - Rajkumar Sasidharan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Liudmilla Rubbi
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Yuko Fujiwara
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute Harvard Stem Cell Institute Harvard Medical School, Boston, MA, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Stuart H Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute Harvard Stem Cell Institute Harvard Medical School, Boston, MA, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
| | - Hanna Ka Mikkola
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
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13
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Rogers E, Sasidharan R, Sequeira G, Wood M, Bird S, Arroll B, Stewart J, Keogh J, Macleod R. Accert: Auckland'S Cancer Cachexia Evaluating Resistance Training Study. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu356.74] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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14
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Voesenek LACJ, van Veen H, Sasidharan R. Learning from nature: the use of non-model species to identify novel acclimations to flooding stress. AoB Plants 2014; 6:plu016. [PMID: 24876298 PMCID: PMC4011469 DOI: 10.1093/aobpla/plu016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 03/17/2014] [Indexed: 05/18/2023]
Abstract
Excess water in the form of waterlogged soil or deeper submergence (generically termed 'flooding') influences plant growth, survival and species distribution in many natural ecosystems. It also has a negative impact on crop growth and yield since many agricultural species are flooding intolerant. The often devastating effect of flooding on plant performance is related to its interference with gas exchange between the plant and its environment. This results in energy deficiency and carbohydrate starvation. In the near future, flooding frequency is expected to increase due to global climate change and the human population is expected to increase to ∼9 billion people by 2050. The need for increased agricultural productivity is self-evident and this will require a better mechanistic understanding of the interaction between plants and abiotic stresses such as flooding. We argue that, in seeking this understanding, we should not restrict the research to model species such as rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana). This is because some stress-tolerance mechanisms are not found in these species. Examples are given of how flooding tolerance is achieved by non-model species of Rumex and Rorippa that have evolved to cope with flooding in natural environments. These findings will add usefully to the spread of resources available to plant breeding programmes aimed at improving flooding tolerance in crop plants.
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Affiliation(s)
- L A C J Voesenek
- Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - H van Veen
- Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - R Sasidharan
- Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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15
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Org T, Duan D, Ferrari R, Montel-Hagen A, Van Handel B, Sasidharan R, Orkin SH, Kurdistani S, Mikkola HK. Abstract 356: Scl Represses Cardiogenesis via Distant Enhancers during Hemogenic Endothelium Specification. Circ Res 2013. [DOI: 10.1161/res.113.suppl_1.a356] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Understanding the mechanisms directing mesoderm specification holds a great potential to advance the development of cell-based therapies for cardiovascular and blood disorders. The bHLH transcription factor Scl is known as the master regulator of the hematopoietic fate. We recently discovered that, in addition to its critical function in promoting the establishment of hemogenic endothelium during hematopoietic stem/progenitor cell (HS/PC) development, Scl is also required to repress cardiomyogenesis in endothelium in hematopoietic tissues and endocardium in the heart. However, the mechanisms for the cardiac repression have remained unknown.
Using ChIP-sequencing and microarray analysis of Flk+ mesoderm differentiated from mouse ES cells, we show that Scl both directly activates a broad gene regulatory network required for hemogenic endothelium and HS/PC development (e.g. Runx1, cMyb, Lyl1, Mef2C, Sox7 etc.), and directly represses transcriptional regulators required for cardiogenesis (e.g. Gata4, Gata6, Myocd, etc.) and mesoderm development (Eomes, Mixl1, Etv2, etc.). Repression of cardiac and mesodermal programs occurs during a short developmental window through Scl binding to distant enhancers, while binding to hematopoietic regulators extends throughout HS/PC and red blood cell development and encompasses both distant and proximal binding sites. We also discovered that, surprisingly, Scl complex partners Gata 1 and 2 are dispensable for hematopoietic vs. cardiac specification and Scl binding to majority of its target genes. Nevertheless, Gata factors co-operate with Scl to activate selected transcription factors that facilitate HS/PC emergence from hemogenic endothelium. These results denote Scl as a true master regulator of hematopoietic vs. cardiac fate choice and suggest a mechanism by which lineage-specific bHLH factors direct the divergence of competing fates.
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Affiliation(s)
- Tonis Org
- Dept of Molecular, Cell and Developmental Biology, Univ of California, Los Angeles, Los Angeles, CA
| | - Dan Duan
- Dept of Molecular, Cell and Developmental Biology, Univ of California, Los Angeles, Los Angeles, CA
| | - Roberto Ferrari
- Dept of Biological Chemistry, Univ of California, Los Angeles, Los Angeles, CA
| | - Amelie Montel-Hagen
- Dept of Molecular, Cell and Developmental Biology, Univ of California, Los Angeles, Los Angeles, CA
| | - Ben Van Handel
- Dept of Molecular, Cell and Developmental Biology, Univ of California, Los Angeles, Los Angeles, CA
| | - Rajkumar Sasidharan
- Dept of Molecular, Cell and Developmental Biology, Univ of California, Los Angeles, Los Angeles, CA
| | - Stuart H Orkin
- Dept of Pediatric Oncology, Dana-Farber Cancer Institute and Div of Hematology/Oncology, Children’s Hosp Boston, Harvard Stem Cell Institute, Harvard Med Sch, Boston, Los Angeles, CA
| | - Siavash Kurdistani
- Dept of Biological Chemistry, Univ of California; Eli and Edythe Broad Stem Cell Rsch Cntr, Univ of California, Los Angeles, Los Angeles, CA
| | - Hanna K Mikkola
- Dept of Molecular, Cell and Developmental Biology, Univ of California, Los Angeles; Eli and Edythe Broad Stem Cell Rsch Cntr, Univ of California, Los Angeles, Los Angeles, CA
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16
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Nakano H, Liu X, Arshi A, van Handel B, Sasidharan R, Harmon AW, Shin JH, Schwartz RJ, Conway SJ, Harvey RP, Pashmforoush M, Mikkola HK, Nakano A. Abstract 290: Haemogenic Endocardium Contribute To Definitive Hematopoiesis During Cardiogenesis. Circ Res 2013. [DOI: 10.1161/res.113.suppl_1.a290] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The circulatory system is the first functional organ system that develops during mammalian life. Accumulating evidences suggest that cardiac and endocardial cells can arise from a single common progenitor cell during mammalian cardiogenesis. Notably, these early cardiac progenitors express multiple hematopoietic transcription factors, consistent with previous reports. Indeed, a close relationship among cardiac, endocardial and hematopoietic lineages has been suggested in fly, zebrafish, and embryonic stem cell in vitro differentiation models. However, it is unclear when, where and how this hematopoietic gene program is in operation during in vivo mammalian cardiogenesis. Hematopoietic colony assay suggests that mouse heart explants generate myeloids and erythroids in the absence of circulation, suggesting that the heart tube is a de novo site for the definitive hematopoiesis. Lineage tracing revealed that putative cardiac-derived Nkx2-5+/Isl1+ endocardial cells give rise to CD41+ hematopoietic progenitors that contribute to definitive hematopoiesis in vivo and ex vivo during embryogenesis earlier than in the AGM region. Furthermore, Nkx2-5 and Isl1 are both required for the hemogenic activity of the endocardium. Together, identification of Nkx2-5/Isl1-dependent hemogenic endocardial cells (1) adds hematopoietic component in the cardiogenesis lineage tree, (2) changes the long-held dogma that AGM is the only major source of definitive hematopoiesis in the embryo proper, and (3) represents phylogenetically conserved fundamental mechanism of cardio-vasculo-hematopoietic differentiation pathway during the development of circulatory system.
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Duan D, Org T, Ferrari R, Montel-Hagen A, van Handel B, Sasidharan R, Fujiwara Y, Orkin S, Kurdistani S, Mikkola H. Scl represses cardiogenesis via distant enhancers during hemogenic endothelium specification. Exp Hematol 2013. [DOI: 10.1016/j.exphem.2013.05.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Voesenek LACJ, Sasidharan R. Ethylene--and oxygen signalling--drive plant survival during flooding. Plant Biol (Stuttg) 2013; 15:426-35. [PMID: 23574304 DOI: 10.1111/plb.12014] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/12/2013] [Indexed: 05/20/2023]
Abstract
Flooding is a widely occurring environmental stress both for natural and cultivated plant species. The primary problems associated with flooding arise due to restricted gas diffusion underwater. This hampers gas exchange needed for the critical processes of photosynthesis and respiration. Plant acclimation to flooding includes the adaptation of a suite of traits that helps alleviate or avoid these stressful conditions and improves or restores exchange of O2 and CO2 . The manifestation of these traits is, however, reliant on the timely perception of signals that convey the underwater status. Flooding-associated reduced gas diffusion imposes a drastic change in the internal gas composition within submerged plant organs. One of the earliest changes is an increase in the levels of the gaseous plant hormone ethylene. Depending on the species, organ, flooding conditions and time of the day, plants will also subsequently experience a reduction in oxygen levels. This review provides a comprehensive overview on the roles of ethylene and oxygen as critical signals of flooding stress. It includes a discussion of the dynamics of these gases in plants when underwater, their interaction, current knowledge of their perception mechanisms and the resulting downstream changes that mediate important acclimative processes that allow endurance and survival under flooded conditions.
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Affiliation(s)
- L A C J Voesenek
- Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
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Affiliation(s)
- R Sasidharan
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH Utrecht, the Netherlands
- Centre for Biosystems Genomics, 6708, PD Wageningen, the Netherlands
| | - L A C J Voesenek
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH Utrecht, the Netherlands
- Centre for Biosystems Genomics, 6708, PD Wageningen, the Netherlands
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Magnusson M, Sierra MI, Sasidharan R, Prashad SL, Romero M, Saarikoski P, Van Handel B, Huang A, Li X, Mikkola HKA. Expansion on stromal cells preserves the undifferentiated state of human hematopoietic stem cells despite compromised reconstitution ability. PLoS One 2013; 8:e53912. [PMID: 23342037 PMCID: PMC3547050 DOI: 10.1371/journal.pone.0053912] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [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: 08/21/2012] [Accepted: 12/04/2012] [Indexed: 12/15/2022] Open
Abstract
Lack of HLA-matched hematopoietic stem cells (HSC) limits the number of patients with life-threatening blood disorders that can be treated by HSC transplantation. So far, insufficient understanding of the regulatory mechanisms governing human HSC has precluded the development of effective protocols for culturing HSC for therapeutic use and molecular studies. We defined a culture system using OP9M2 mesenchymal stem cell (MSC) stroma that protects human hematopoietic stem/progenitor cells (HSPC) from differentiation and apoptosis. In addition, it facilitates a dramatic expansion of multipotent progenitors that retain the immunophenotype (CD34+CD38-CD90+) characteristic of human HSPC and proliferative potential over several weeks in culture. In contrast, transplantable HSC could be maintained, but not significantly expanded, during 2-week culture. Temporal analysis of the transcriptome of the ex vivo expanded CD34+CD38-CD90+ cells documented remarkable stability of most transcriptional regulators known to govern the undifferentiated HSC state. Nevertheless, it revealed dynamic fluctuations in transcriptional programs that associate with HSC behavior and may compromise HSC function, such as dysregulation of PBX1 regulated genetic networks. This culture system serves now as a platform for modeling human multilineage hematopoietic stem/progenitor cell hierarchy and studying the complex regulation of HSC identity and function required for successful ex vivo expansion of transplantable HSC.
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Affiliation(s)
- Mattias Magnusson
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Maria I. Sierra
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Rajkumar Sasidharan
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Sacha L. Prashad
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Melissa Romero
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Pamela Saarikoski
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Ben Van Handel
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Andy Huang
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Xinmin Li
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Hanna K. A. Mikkola
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
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21
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Nakano H, Nakano H, Liu X, Arshi A, Nakashima Y, van Handel B, Sasidharan R, Harmon AW, Shin JH, Schwartz RJ, Conway SJ, Harvey RP, Pashmforoush M, Mikkola HKA, Nakano A. Haemogenic endocardium contributes to transient definitive haematopoiesis. Nat Commun 2013; 4:1564. [PMID: 23463007 PMCID: PMC3612528 DOI: 10.1038/ncomms2569] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [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: 09/19/2012] [Accepted: 01/31/2013] [Indexed: 12/11/2022] Open
Abstract
Haematopoietic cells arise from spatiotemporally restricted domains in the developing embryo. Although studies of non-mammalian animal and in vitro embryonic stem cell models suggest a close relationship among cardiac, endocardial and haematopoietic lineages, it remains unknown whether the mammalian heart tube serves as a haemogenic organ akin to the dorsal aorta. Here we examine the haemogenic activity of the developing endocardium. Mouse heart explants generate myeloid and erythroid colonies in the absence of circulation. Haemogenic activity arises from a subset of endocardial cells in the outflow cushion and atria earlier than in the aorta-gonad-mesonephros region, and is transient and definitive in nature. Interestingly, key cardiac transcription factors, Nkx2-5 and Isl1, are expressed in and required for the haemogenic population of the endocardium. Together, these data suggest that a subset of endocardial/endothelial cells serve as a de novo source for transient definitive haematopoietic progenitors.
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Affiliation(s)
- Haruko Nakano
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Haruko Nakano
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xiaoqian Liu
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Armin Arshi
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yasuhiro Nakashima
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ben van Handel
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rajkumar Sasidharan
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Andrew W. Harmon
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jae-Ho Shin
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Robert J. Schwartz
- Department of Biology and Biochemistry, University of Houston, Houston, 77204, USA
| | - Simon J. Conway
- Departments of Anatomy & Cell Biology, Medical & Molecular Genetics, Biochemistry & Molecular Biology, Indianapolis, IN 46202, USA
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Richard P. Harvey
- Developmental Biology Division, the Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Australia
| | - Mohammad Pashmforoush
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California Keck School of Medicine, 90089
| | - Hanna K. A. Mikkola
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Atsushi Nakano
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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22
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Van Handel B, Montel-Hagen A, Sasidharan R, Nakano H, Ferrari R, Boogerd CJ, Schredelseker J, Wang Y, Hunter S, Org T, Zhou J, Li X, Pellegrini M, Chen JN, Orkin SH, Kurdistani SK, Evans SM, Nakano A, Mikkola HKA. Scl represses cardiomyogenesis in prospective hemogenic endothelium and endocardium. Cell 2012; 150:590-605. [PMID: 22863011 DOI: 10.1016/j.cell.2012.06.026] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Revised: 04/13/2012] [Accepted: 06/01/2012] [Indexed: 01/12/2023]
Abstract
Endothelium in embryonic hematopoietic tissues generates hematopoietic stem/progenitor cells; however, it is unknown how its unique potential is specified. We show that transcription factor Scl/Tal1 is essential for both establishing the hematopoietic transcriptional program in hemogenic endothelium and preventing its misspecification to a cardiomyogenic fate. Scl(-/-) embryos activated a cardiac transcriptional program in yolk sac endothelium, leading to the emergence of CD31+Pdgfrα+ cardiogenic precursors that generated spontaneously beating cardiomyocytes. Ectopic cardiogenesis was also observed in Scl(-/-) hearts, where the disorganized endocardium precociously differentiated into cardiomyocytes. Induction of mosaic deletion of Scl in Scl(fl/fl)Rosa26Cre-ER(T2) embryos revealed a cell-intrinsic, temporal requirement for Scl to prevent cardiomyogenesis from endothelium. Scl(-/-) endothelium also upregulated the expression of Wnt antagonists, which promoted rapid cardiomyocyte differentiation of ectopic cardiogenic cells. These results reveal unexpected plasticity in embryonic endothelium such that loss of a single master regulator can induce ectopic cardiomyogenesis from endothelial cells.
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Affiliation(s)
- Ben Van Handel
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Abstract
We have developed GFam, a platform for automatic annotation of gene/protein families. GFam provides a framework for genome initiatives and model organism resources to build domain-based families, derive meaningful functional labels and offers a seamless approach to propagate functional annotation across periodic genome updates. GFam is a hybrid approach that uses a greedy algorithm to chain component domains from InterPro annotation provided by its 12 member resources followed by a sequence-based connected component analysis of un-annotated sequence regions to derive consensus domain architecture for each sequence and subsequently generate families based on common architectures. Our integrated approach increases sequence coverage by 7.2 percentage points and residue coverage by 14.6 percentage points higher than the coverage relative to the best single-constituent database within InterPro for the proteome of Arabidopsis. The true power of GFam lies in maximizing annotation provided by the different InterPro data sources that offer resource-specific coverage for different regions of a sequence. GFam’s capability to capture higher sequence and residue coverage can be useful for genome annotation, comparative genomics and functional studies. GFam is a general-purpose software and can be used for any collection of protein sequences. The software is open source and can be obtained from http://www.paccanarolab.org/software/gfam/.
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Affiliation(s)
- Rajkumar Sasidharan
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
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Ferrari R, Su T, Li B, Bonora G, Oberai A, Chan Y, Sasidharan R, Berk AJ, Pellegrini M, Kurdistani SK. Reorganization of the host epigenome by a viral oncogene. Genome Res 2012; 22:1212-21. [PMID: 22499665 PMCID: PMC3396363 DOI: 10.1101/gr.132308.111] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [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] [Indexed: 12/12/2022]
Abstract
Adenovirus small e1a oncoprotein causes ∼70% reduction in cellular levels of histone H3 lysine 18 acetylation (H3K18ac). It is unclear, however, where this dramatic reduction occurs genome-wide. ChIP-sequencing revealed that by 24 h after expression, e1a erases 95% of H3K18ac peaks in normal, contact-inhibited fibroblasts and replaces them with one-third as many at new genomic locations. The H3K18ac peaks at promoters and intergenic regions of genes with fibroblast-related functions are eliminated after infection, and new H3K18ac peaks are established at promoters of highly induced genes that regulate cell cycling and at new putative enhancers. Strikingly, the regions bound by the retinoblastoma family of proteins in contact-inhibited fibroblasts gain new peaks of H3K18ac in the e1a-expressing cells, including 55% of RB1-bound loci. In contrast, over half of H3K9ac peaks are similarly distributed before and after infection, independently of RB1. The strategic redistribution of H3K18ac by e1a highlights the importance of this modification for transcriptional activation and cellular transformation as well as functional differences between the RB-family member proteins.
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Affiliation(s)
- Roberto Ferrari
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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25
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Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 2011; 40:D1202-10. [PMID: 22140109 PMCID: PMC3245047 DOI: 10.1093/nar/gkr1090] [Citation(s) in RCA: 1414] [Impact Index Per Article: 108.8] [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] [Indexed: 12/11/2022] Open
Abstract
The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is a genome database for Arabidopsis thaliana, an important reference organism for many fundamental aspects of biology as well as basic and applied plant biology research. TAIR serves as a central access point for Arabidopsis data, annotates gene function and expression patterns using controlled vocabulary terms, and maintains and updates the A. thaliana genome assembly and annotation. TAIR also provides researchers with an extensive set of visualization and analysis tools. Recent developments include several new genome releases (TAIR8, TAIR9 and TAIR10) in which the A. thaliana assembly was updated, pseudogenes and transposon genes were re-annotated, and new data from proteomics and next generation transcriptome sequencing were incorporated into gene models and splice variants. Other highlights include progress on functional annotation of the genome and the release of several new tools including Textpresso for Arabidopsis which provides the capability to carry out full text searches on a large body of research literature.
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Affiliation(s)
- Philippe Lamesch
- Department of Plant Biology, Carnegie Institution, 260 Panama St, Stanford, CA 94305, USA
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Vashisht D, Hesselink A, Pierik R, Ammerlaan JMH, Bailey-Serres J, Visser EJW, Pedersen O, van Zanten M, Vreugdenhil D, Jamar DCL, Voesenek LACJ, Sasidharan R. Natural variation of submergence tolerance among Arabidopsis thaliana accessions. New Phytol 2011; 190:299-310. [PMID: 21108648 DOI: 10.1111/j.1469-8137.2010.03552.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
• The exploitation of natural variation in Arabidopsis thaliana (Arabidopsis) provides a huge potential for the identification of the molecular mechanisms underlying this variation as a result of the availability of a vast array of genetic and genomic resources for this species. Eighty-six Arabidopsis accessions were screened for natural variation in flooding tolerance. This forms the first step towards the identification and characterization of the role of candidate genes contributing to flooding tolerance. • Arabidopsis accessions at the 10-leaf stage were subjected to complete submergence in the dark. Survival curves were plotted to estimate median lethal times as a measure of tolerance. Flooding-associated survival parameters, such as root and shoot oxygen content, initial carbohydrate content and petiole elongation under water, were also measured. • There was a significant variation in submergence tolerance among Arabidopsis accessions. However, the order of tolerance did not correlate with root and shoot oxygen content or initial amounts of shoot starch and total soluble sugars. A negative correlation was observed between submergence tolerance and underwater petiole elongation. • Arabidopsis accessions show considerable variation in the ability to tolerate complete submergence, making it a good species in which to identify and characterize genes and to study mechanisms that contribute to survival under water.
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Affiliation(s)
- D Vashisht
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands
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27
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Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 2010; 330:1775-87. [PMID: 21177976 PMCID: PMC3142569 DOI: 10.1126/science.1196914] [Citation(s) in RCA: 741] [Impact Index Per Article: 52.9] [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] [Indexed: 12/26/2022]
Abstract
We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.
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Affiliation(s)
- Mark B. Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, 51 Prospect Street, New Haven, CT 06511, USA
| | - Zhi John Lu
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Eric L. Van Nostrand
- Department of Genetics, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Chao Cheng
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Bradley I. Arshinoff
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
- Department of Molecular Genetics, University of Toronto, 27 King's College Circle, Toronto, Ontario M5S 1A1, Canada
| | - Tao Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
- Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Kevin Y. Yip
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Rebecca Robilotto
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Andreas Rechtsteiner
- Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kohta Ikegami
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pedro Alves
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Aurelien Chateigner
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Marc Perry
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Mitzi Morris
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
| | - Raymond K. Auerbach
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Xin Feng
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
- Department of Biomedical Engineering, State University of New York at Stonybrook, Stonybrook, NY 11794, USA
| | - Jing Leng
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Anne Vielle
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Wei Niu
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06824, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Kahn Rhrissorrakrai
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
| | - Ashish Agarwal
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, 51 Prospect Street, New Haven, CT 06511, USA
| | - Roger P. Alexander
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Galt Barber
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064 USA
| | - Cathleen M. Brdlik
- Department of Genetics, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Jennifer Brennan
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Adrian Carr
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Ming-Sin Cheung
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Hiram Clawson
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064 USA
| | - Sergio Contrino
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | | | - Abby F. Dernburg
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA, and Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Arshad Desai
- Ludwig Institute Cancer Research/Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0653, USA
| | - Lindsay Dick
- David Rockefeller Graduate Program, Rockefeller University, 1230 York Avenue New York, NY 10065, USA
| | - Andréa C. Dosé
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA, and Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jiang Du
- Department of Computer Science, Yale University, 51 Prospect Street, New Haven, CT 06511, USA
| | - Thea Egelhofer
- Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Sevinc Ercan
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ghia Euskirchen
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06824, USA
| | - Brent Ewing
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Elise A. Feingold
- Division of Extramural Research, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Reto Gassmann
- Ludwig Institute Cancer Research/Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0653, USA
| | - Peter J. Good
- Division of Extramural Research, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Phil Green
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Francois Gullier
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Michelle Gutwein
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
| | - Mark S. Guyer
- Division of Extramural Research, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Lukas Habegger
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Ting Han
- Life Sciences Institute, Department of Human Genetics, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109–2216, USA
| | - Jorja G. Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Stefan R. Henz
- Max Planck Institute for Developmental Biology, Spemannstrasse 37-39, 72076 Tübingen, Germany
| | - Angie Hinrichs
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064 USA
| | - Heather Holster
- Roche NimbleGen, 500 South Rosa Road, Madison, WI 53719, USA
| | - Tony Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - A. Leo Iniguez
- Roche NimbleGen, 500 South Rosa Road, Madison, WI 53719, USA
| | - Judith Janette
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Morten Jensen
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Masaomi Kato
- Department of Molecular, Cellular and Developmental Biology, Post Office Box 208103, Yale University, New Haven, CT 06520, USA
| | - W. James Kent
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064 USA
| | - Ellen Kephart
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Vishal Khivansara
- Life Sciences Institute, Department of Human Genetics, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109–2216, USA
| | - Ekta Khurana
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - John K. Kim
- Life Sciences Institute, Department of Human Genetics, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109–2216, USA
| | - Paulina Kolasinska-Zwierz
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Eric C. Lai
- Sloan-Kettering Institute, 1275 York Avenue, Post Office Box 252, New York, NY 10065, USA
| | - Isabel Latorre
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Amber Leahey
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Suzanna Lewis
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720 USA
| | - Paul Lloyd
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Lucas Lochovsky
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Rebecca F. Lowdon
- Division of Extramural Research, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Yaniv Lubling
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Rachel Lyne
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Michael MacCoss
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Sebastian D. Mackowiak
- Max-Delbrück-Centrum für Molekulare Medizin, Division of Systems Biology, Robert-Rössle-Strasse 10, D-13125 Berlin-Buch, Germany
| | - Marco Mangone
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
| | - Sheldon McKay
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11542 USA
| | - Desirea Mecenas
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
| | - Gennifer Merrihew
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - David M. Miller
- Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37232–8240, USA
| | - Andrew Muroyama
- Ludwig Institute Cancer Research/Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0653, USA
| | - John I. Murray
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Siew-Loon Ooi
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Hoang Pham
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA, and Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Taryn Phippen
- Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Elicia A. Preston
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Nikolaus Rajewsky
- Max-Delbrück-Centrum für Molekulare Medizin, Division of Systems Biology, Robert-Rössle-Strasse 10, D-13125 Berlin-Buch, Germany
| | - Gunnar Rätsch
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany
| | - Heidi Rosenbaum
- Roche NimbleGen, 500 South Rosa Road, Madison, WI 53719, USA
| | - Joel Rozowsky
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Kim Rutherford
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Peter Ruzanov
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Rajkumar Sasidharan
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Andrea Sboner
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Paul Scheid
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Hyunjin Shin
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
- Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Chong Shou
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Frank J. Slack
- Department of Molecular, Cellular and Developmental Biology, Post Office Box 208103, Yale University, New Haven, CT 06520, USA
| | - Cindie Slightam
- Department of Developmental Biology, Stanford University Medical Center, 279 Campus Drive, Stanford, CA 94305–5329, USA
| | - Richard Smith
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - William C. Spencer
- Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37232–8240, USA
| | - E. O. Stinson
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720 USA
| | - Scott Taing
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
| | - Teruaki Takasaki
- Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Dionne Vafeados
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Ksenia Voronina
- Ludwig Institute Cancer Research/Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0653, USA
| | - Guilin Wang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Nicole L. Washington
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720 USA
| | - Christina M. Whittle
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Beijing Wu
- Department of Developmental Biology, Stanford University Medical Center, 279 Campus Drive, Stanford, CA 94305–5329, USA
| | - Koon-Kiu Yan
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Georg Zeller
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Zheng Zha
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Mei Zhong
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06824, USA
| | - Xingliang Zhou
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Julie Ahringer
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Susan Strome
- Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kristin C. Gunsalus
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
- New York University, Abu Dhabi, United Arab Emirates
| | - Gos Micklem
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - X. Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
- Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Valerie Reinke
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Stuart K. Kim
- Department of Genetics, Stanford University Medical Center, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University Medical Center, 279 Campus Drive, Stanford, CA 94305–5329, USA
| | - LaDeana W. Hillier
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Fabio Piano
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
- New York University, Abu Dhabi, United Arab Emirates
| | - Michael Snyder
- Department of Genetics, Stanford University Medical Center, Stanford, CA 94305, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06824, USA
| | - Lincoln Stein
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
- Department of Molecular Genetics, University of Toronto, 27 King's College Circle, Toronto, Ontario M5S 1A1, Canada
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11542 USA
| | - Jason D. Lieb
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert H. Waterston
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
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Agarwal A, Koppstein D, Rozowsky J, Sboner A, Habegger L, Hillier LW, Sasidharan R, Reinke V, Waterston RH, Gerstein M. Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. BMC Genomics 2010; 11:383. [PMID: 20565764 PMCID: PMC3091629 DOI: 10.1186/1471-2164-11-383] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [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: 12/30/2009] [Accepted: 06/17/2010] [Indexed: 11/25/2022] Open
Abstract
Background Tiling arrays have been the tool of choice for probing an organism's transcriptome without prior assumptions about the transcribed regions, but RNA-Seq is becoming a viable alternative as the costs of sequencing continue to decrease. Understanding the relative merits of these technologies will help researchers select the appropriate technology for their needs. Results Here, we compare these two platforms using a matched sample of poly(A)-enriched RNA isolated from the second larval stage of C. elegans. We find that the raw signals from these two technologies are reasonably well correlated but that RNA-Seq outperforms tiling arrays in several respects, notably in exon boundary detection and dynamic range of expression. By exploring the accuracy of sequencing as a function of depth of coverage, we found that about 4 million reads are required to match the sensitivity of two tiling array replicates. The effects of cross-hybridization were analyzed using a "nearest neighbor" classifier applied to array probes; we describe a method for determining potential "black list" regions whose signals are unreliable. Finally, we propose a strategy for using RNA-Seq data as a gold standard set to calibrate tiling array data. All tiling array and RNA-Seq data sets have been submitted to the modENCODE Data Coordinating Center. Conclusions Tiling arrays effectively detect transcript expression levels at a low cost for many species while RNA-Seq provides greater accuracy in several regards. Researchers will need to carefully select the technology appropriate to the biological investigations they are undertaking. It will also be important to reconsider a comparison such as ours as sequencing technologies continue to evolve.
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Affiliation(s)
- Ashish Agarwal
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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Abstract
Breast cancer is one of the most commonly diagnosed malignancies during pregnancy. Pregnancy-associated breast cancer (PABC) presents a challenging clinical situation. This article reviews the current evidence around the management of PABC and the safety of pregnancy after breast cancer. The trend towards later age at first childbirth has resulted in an increase in the number of breast cancer cases coexistent with pregnancy. The management of breast cancer during pregnancy requires a multidisciplinary team approach. Breast surgery can be safely performed during any trimester of pregnancy. Radiation therapy, if required, must be delayed until after delivery. The majority of patients with PABC require chemotherapy. The timing of delivery in relation to chemotherapy administration should be carefully considered. There is no evidence to date that pregnancy termination influences overall survival for the mother. To date, there is no clear evidence that subsequent pregnancy after breast cancer is associated with worse maternal survival. There is a suggestion that subsequent pregnancy may in fact be associated with an improved survival. However, the available studies are limited by potential biases.
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Affiliation(s)
- R Sasidharan
- Department of Medical Oncology, Auckland City Hospital , Auckland , New Zealand
| | - V Harvey
- Department of Medical Oncology, Auckland City Hospital , Auckland , New Zealand
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Lamesch P, Dreher K, Swarbreck D, Sasidharan R, Reiser L, Huala E. Using The
Arabidopsis
Information Resource (TAIR) to Find Information About
Arabidopsis
Genes. ACTA ACUST UNITED AC 2010; Chapter 1:1.11.1-1.11.51. [DOI: 10.1002/0471250953.bi0111s30] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Kate Dreher
- Carnegie Institution for Science Stanford California
| | | | | | | | - Eva Huala
- Carnegie Institution for Science Stanford California
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Nepusz T, Sasidharan R, Paccanaro A. SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale. BMC Bioinformatics 2010; 11:120. [PMID: 20214776 PMCID: PMC2841596 DOI: 10.1186/1471-2105-11-120] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [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: 11/25/2009] [Accepted: 03/09/2010] [Indexed: 11/10/2022] Open
Abstract
Background An important problem in genomics is the automatic inference of groups of homologous proteins from pairwise sequence similarities. Several approaches have been proposed for this task which are "local" in the sense that they assign a protein to a cluster based only on the distances between that protein and the other proteins in the set. It was shown recently that global methods such as spectral clustering have better performance on a wide variety of datasets. However, currently available implementations of spectral clustering methods mostly consist of a few loosely coupled Matlab scripts that assume a fair amount of familiarity with Matlab programming and hence they are inaccessible for large parts of the research community. Results SCPS (Spectral Clustering of Protein Sequences) is an efficient and user-friendly implementation of a spectral method for inferring protein families. The method uses only pairwise sequence similarities, and is therefore practical when only sequence information is available. SCPS was tested on difficult sets of proteins whose relationships were extracted from the SCOP database, and its results were extensively compared with those obtained using other popular protein clustering algorithms such as TribeMCL, hierarchical clustering and connected component analysis. We show that SCPS is able to identify many of the family/superfamily relationships correctly and that the quality of the obtained clusters as indicated by their F-scores is consistently better than all the other methods we compared it with. We also demonstrate the scalability of SCPS by clustering the entire SCOP database (14,183 sequences) and the complete genome of the yeast Saccharomyces cerevisiae (6,690 sequences). Conclusions Besides the spectral method, SCPS also implements connected component analysis and hierarchical clustering, it integrates TribeMCL, it provides different cluster quality tools, it can extract human-readable protein descriptions using GI numbers from NCBI, it interfaces with external tools such as BLAST and Cytoscape, and it can produce publication-quality graphical representations of the clusters obtained, thus constituting a comprehensive and effective tool for practical research in computational biology. Source code and precompiled executables for Windows, Linux and Mac OS X are freely available at http://www.paccanarolab.org/software/scps.
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Affiliation(s)
- Tamás Nepusz
- Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, TW20 0EX, Egham, UK.
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Sasidharan R, Agarwal A, Rozowsky J, Gerstein M. An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping. BMC Res Notes 2009; 2:150. [PMID: 19630981 PMCID: PMC2764720 DOI: 10.1186/1756-0500-2-150] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [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: 01/31/2009] [Accepted: 07/24/2009] [Indexed: 11/24/2022] Open
Abstract
Background There are two main technologies for transcriptome profiling, namely, tiling microarrays and high-throughput sequencing. Recently there has been a tremendous amount of excitement about the latter because of the advent of next-generation sequencing technologies and its promises. Consequently, the question of the moment is how these two technologies compare. Here we attempt to develop an approach to do a fair comparison of transcripts identified from tiling microarray and MPSS sequencing data. Findings This comparison is a challenging task because the sequencing data is discrete while the tiling array data is continuous. We use the published rice and Arabidopsis datasets which provide currently best matched sets of arrays and sequencing experiments using a slightly earlier generation of sequencing, the MPSS tag sequencing technology. After scoring the arrays consistently in both the organisms, a first pass comparison reveals a surprisingly small overlap in transcripts of 22% and 66% respectively, in rice and Arabidopsis. However, when we do the analysis in detail, we find that this is an underestimate. In particular, when we map the probe intensities onto the sequencing tags and then look at their intensity distribution, we see that they are very similar to exons. Furthermore, restricting our comparison to only protein-coding gene loci revealed a very good overlap between the two technologies. Conclusion Our approach to compare genome tiling microarray and MPSS sequencing data suggests that there is actually a reasonable overlap in transcripts identified by the two technologies. This overlap is distorted by the scoring and thresholding in the tiling array scoring procedure.
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Affiliation(s)
- Rajkumar Sasidharan
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA.
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Sasidharan R, Agarwal A, Rozowsky J, Gerstein M. An approach to compare genome tiling microarray and MPSS sequencing data for transcript mapping. BMC Res Notes 2009. [PMCID: PMC2770075 DOI: 10.1186/1756-0500-2-211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We are correcting the abstract of our published article ([1]). The sentence that starts "We observe that 4.5% of MPSS tags...." was not scientifically complete in the original abstract, having only two of the four numbers required to describe a comparison of two technologies in two different organisms. The abstract below more accurately describes our findings, as documented in Figure 1 of the manuscript.
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Abstract
Recently, there was a report that explored the oxygen content of transmembrane proteins over macroevolutionary time scales where the authors observed a correlation between the geological time of appearance of compartmentalized cells with atmospheric oxygen concentration. The authors predicted, characterized and correlated the differences in the structure and composition of transmembrane proteins from the three kingdoms of life with atmospheric oxygen concentrations in geological timescale. They hypothesized that transmembrane proteins in ancient taxa were selectively excluding oxygen and as this constraint relaxed over time with increase in the levels of atmospheric oxygen the size and number of communication-related transmembrane proteins increased. In summary, they concluded that compartmentalized and non-compartmentalized cells can be distinguished by how oxygen is partitioned at the proteome level. They derived this conclusion from an analysis of 19 taxa. We extended their analysis on a larger sample of taxa comprising 309 eubacterial, 34 archaeal, and 30 eukaryotic complete proteomes and observed that one can not absolutely separate the two groups of cells based on partition of oxygen in their membrane proteins. In addition, the origin of compartmentalized cells is likely to have been driven by an innovation than happened 2700 million years ago in the membrane composition of cells that led to the evolution of endocytosis and exocytosis rather than due to the rise in concentration of atmospheric oxygen.
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Affiliation(s)
- Rajkumar Sasidharan
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut, United States of America
| | - Andrew Smith
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
| | - Mark Gerstein
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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Sasidharan R. Infections Causing Human Cancer. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2008. [PMCID: PMC2442730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Rajkumar Sasidharan
- Yale University School of Medicine, Molecular Biophysics and Biochemistry Department
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Abstract
We have determined the general constraints that govern sequence divergence in proteins that retain entirely, or very largely, the same structure and function. To do this we collected data from three different groups of orthologous sequences: those found in humans and mice, in humans and chickens, and in Escherichia coli and Salmonella enterica. In total, these organisms have 21,738 suitable pairs of orthologs, and these contain nearly 2 million mutations. The three groups differ greatly in the taxa from which they come and/or in the time that separates them from their last common ancestor. Nevertheless, the results we obtain from the three different groups are strikingly similar. For each group, the orthologous sequence pairs were assigned to six different divergence categories on the basis of their sequence identities. For categories with the same divergence, common accepted mutations have similar frequencies and rank orders in the three groups. With divergence, the width of the range of common mutations grows in the same manner in each group. We examined the distribution of mutations in protein structures. With increasing divergence, mutations increase at different rates in the buried, intermediate, and exposed regions of protein structures in a manner that explains the exponential relationship between the divergence of structure and sequence. This work implies that commonly allowed mutations are selected by a set of general constraints that are well defined and whose nature varies with divergence.
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Affiliation(s)
- Rajkumar Sasidharan
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, United Kingdom.
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Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Wang Deng X. Global identification and characterization of transcriptionally active regions in the rice genome. PLoS One 2007; 2:e294. [PMID: 17372628 PMCID: PMC1808428 DOI: 10.1371/journal.pone.0000294] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Accepted: 02/21/2007] [Indexed: 11/18/2022] Open
Abstract
Genome tiling microarray studies have consistently documented rich transcriptional activity beyond the annotated genes. However, systematic characterization and transcriptional profiling of the putative novel transcripts on the genome scale are still lacking. We report here the identification of 25,352 and 27,744 transcriptionally active regions (TARs) not encoded by annotated exons in the rice (Oryza. sativa) subspecies japonica and indica, respectively. The non-exonic TARs account for approximately two thirds of the total TARs detected by tiling arrays and represent transcripts likely conserved between japonica and indica. Transcription of 21,018 (83%) japonica non-exonic TARs was verified through expression profiling in 10 tissue types using a re-array in which annotated genes and TARs were each represented by five independent probes. Subsequent analyses indicate that about 80% of the japonica TARs that were not assigned to annotated exons can be assigned to various putatively functional or structural elements of the rice genome, including splice variants, uncharacterized portions of incompletely annotated genes, antisense transcripts, duplicated gene fragments, and potential non-coding RNAs. These results provide a systematic characterization of non-exonic transcripts in rice and thus expand the current view of the complexity and dynamics of the rice transcriptome.
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Affiliation(s)
- Lei Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Xiangfeng Wang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing, China
- Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing, China
| | - Rajkumar Sasidharan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Viktor Stolc
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Genome Research Facility, NASA Ames Research Center, Moffett Field, California, United States of America
| | - Wei Deng
- National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing, China
- Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hang He
- National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing, China
- Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jan Korbel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Xuewei Chen
- Department of Plant Pathology, University of California, Davis, California, United States of America
| | | | - Pamela Ronald
- Department of Plant Pathology, University of California, Davis, California, United States of America
| | - Runsheng Chen
- Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Xing Wang Deng
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- * To whom correspondence should be addressed. E-mail:
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Abstract
Domains are the structural, functional or evolutionary units of proteins. Proteins can comprise a single domain or a combination of domains. In multi-domain proteins, the domains almost always occur end-to-end, i.e., one domain follows the C-terminal end of another domain. However, there are exceptions to this common pattern, where multi-domain proteins are formed by insertion of one domain (insert) into another domain (parent). Here, we provide a quantitative description of known insertions in the Protein Data Bank (PDB). We found that 9% of domain combinations observed in non-redundant PDB are insertions. Although 90% of all insertions involve only one insert, proteins can clearly have multiple (nested, two-domain and three-domain) inserts. We also observed correlations between the structure and function of a domain and its tendency to be found as a parent or an insert. There is a bias in insert position towards the C terminus of parents. We observed that the atomic distance between the N and C terminus of an insert is significantly smaller when compared to the N-to-C distance in a parent context or a single domain context. Insertions are found always to occur in loop regions of parent domains. Our observations regarding the relationship between domain insertions and the structure, function and evolution of proteins have implications for protein engineering.
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Affiliation(s)
- R. Aroul-Selvam
- The Wellcome Trust Sanger Institute, Genome Campus Hinxton, Cambridge CB10 1SA UK
| | - Tim Hubbard
- The Wellcome Trust Sanger Institute, Genome Campus Hinxton, Cambridge CB10 1SA UK
| | - Rajkumar Sasidharan
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
- Corresponding author E-mail address of the corresponding author:
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Abstract
Proteins can be formed by single or multiple domains. The process of recombination at the molecular level has generated a wide variety of multi-domain proteins with specific domain organization to cater to the functional requirements of an organism. The functional and structural costs of inserting a domain into another means that multi-domain proteins are usually formed by covalently linking the N-terminus of one domain to the C-terminus of the preceding domain. While this is true in a large proportion of multi-domain proteins, we find a significant fraction of proteins that are the result of domain insertion. The inserted domain breaks the sequence contiguity of the domain into which it is inserted leading to a novel domain organization. This web resource aims to document domain insertions in known protein structures that are classified in the SCOP database. The web server can be accessed from http://stash.mrc-lmb.cam. ac.uk/DomIns/.
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Affiliation(s)
- R Aroul Selvam
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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