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  • 1
    Online Resource
    Online Resource
    Cold Spring Harbor Laboratory ; 2017
    In:  Genes & Development Vol. 31, No. 19 ( 2017-10-01), p. 1973-1987
    In: Genes & Development, Cold Spring Harbor Laboratory, Vol. 31, No. 19 ( 2017-10-01), p. 1973-1987
    Abstract: The X chromosome provides an ideal model system to study the contribution of RNA–protein interactions in epigenetic regulation. In male flies, roX long noncoding RNAs (lncRNAs) harbor several redundant domains to interact with the ubiquitin ligase male-specific lethal 2 (MSL2) and the RNA helicase Maleless (MLE) for X-chromosomal regulation. However, how these interactions provide the mechanics of spreading remains unknown. By using the uvCLAP (UV cross-linking and affinity purification) methodology, which provides unprecedented information about RNA secondary structures in vivo, we identified the minimal functional unit of roX2 RNA. By using wild-type and various MLE mutant derivatives, including a catalytically inactive MLE derivative, MLE GET , we show that the minimal roX RNA contains two mutually exclusive stem–loops that exist in a peculiar structural arrangement: When one stem–loop is unwound by MLE, an alternate structure can form, likely trapping MLE in this perpetually structured region. We show that this functional unit is necessary for dosage compensation, as mutations that disrupt this formation lead to male lethality. Thus, we propose that roX2 lncRNA contains an MLE-dependent affinity switch to enable reversible interactions of the MSL complex to allow dosage compensation of the X chromosome.
    Type of Medium: Online Resource
    ISSN: 0890-9369 , 1549-5477
    RVK:
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2017
    detail.hit.zdb_id: 1467414-2
    SSG: 12
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  • 2
    In: Nature Cell Biology, Springer Science and Business Media LLC, Vol. 23, No. 7 ( 2021-07), p. 704-717
    Abstract: Haematopoietic stem cells (HSCs) are normally quiescent, but have evolved mechanisms to respond to stress. Here, we evaluate haematopoietic regeneration induced by chemotherapy. We detect robust chromatin reorganization followed by increased transcription of transposable elements (TEs) during early recovery. TE transcripts bind to and activate the innate immune receptor melanoma differentiation-associated protein 5 (MDA5) that generates an inflammatory response that is necessary for HSCs to exit quiescence. HSCs that lack MDA5 exhibit an impaired inflammatory response after chemotherapy and retain their quiescence, with consequent better long-term repopulation capacity. We show that the overexpression of ERV and LINE superfamily TE copies in wild-type HSCs, but not in Mda5 −/− HSCs, results in their cycling. By contrast, after knockdown of LINE1 family copies, HSCs retain their quiescence. Our results show that TE transcripts act as ligands that activate MDA5 during haematopoietic regeneration, thereby enabling HSCs to mount an inflammatory response necessary for their exit from quiescence.
    Type of Medium: Online Resource
    ISSN: 1465-7392 , 1476-4679
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 1494945-3
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2020
    In:  GigaScience Vol. 9, No. 11 ( 2020-11-11)
    In: GigaScience, Oxford University Press (OUP), Vol. 9, No. 11 ( 2020-11-11)
    Abstract: Post-transcriptional regulation via RNA-binding proteins plays a fundamental role in every organism, but the regulatory mechanisms lack important understanding. Nevertheless, they can be elucidated by cross-linking immunoprecipitation in combination with high-throughput sequencing (CLIP-Seq). CLIP-Seq answers questions about the functional role of an RNA-binding protein and its targets by determining binding sites on a nucleotide level and associated sequence and structural binding patterns. In recent years the amount of CLIP-Seq data skyrocketed, urging the need for an automatic data analysis that can deal with different experimental set-ups. However, noncanonical data, new protocols, and a huge variety of tools, especially for peak calling, made it difficult to define a standard. Findings CLIP-Explorer is a flexible and reproducible data analysis pipeline for iCLIP data that supports for the first time eCLIP, FLASH, and uvCLAP data. Individual steps like peak calling can be changed to adapt to different experimental settings. We validate CLIP-Explorer on eCLIP data, finding similar or nearly identical motifs for various proteins in comparison with other databases. In addition, we detect new sequence motifs for PTBP1 and U2AF2. Finally, we optimize the peak calling with 3 different peak callers on RBFOX2 data, discuss the difficulty of the peak-calling step, and give advice for different experimental set-ups. Conclusion CLIP-Explorer finally fills the demand for a flexible CLIP-Seq data analysis pipeline that is applicable to the up-to-date CLIP protocols. The article further shows the limitations of current peak-calling algorithms and the importance of a robust peak detection.
    Type of Medium: Online Resource
    ISSN: 2047-217X
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2708999-X
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  • 4
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 28, No. 5 ( 2018-05), p. 699-713
    Abstract: Alternative splicing generates distinct mRNA isoforms and is crucial for proteome diversity in eukaryotes. The RNA-binding protein (RBP) U2AF2 is central to splicing decisions, as it recognizes 3′ splice sites and recruits the spliceosome. We establish “in vitro iCLIP” experiments, in which recombinant RBPs are incubated with long transcripts, to study how U2AF2 recognizes RNA sequences and how this is modulated by trans -acting RBPs. We measure U2AF2 affinities at hundreds of binding sites and compare in vitro and in vivo binding landscapes by mathematical modeling. We find that trans -acting RBPs extensively regulate U2AF2 binding in vivo, including enhanced recruitment to 3′ splice sites and clearance of introns. Using machine learning, we identify and experimentally validate novel trans -acting RBPs (including FUBP1, CELF6, and PCBP1) that modulate U2AF2 binding and affect splicing outcomes. Our study offers a blueprint for the high-throughput characterization of in vitro mRNP assembly and in vivo splicing regulation.
    Type of Medium: Online Resource
    ISSN: 1088-9051 , 1549-5469
    RVK:
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2018
    detail.hit.zdb_id: 1483456-X
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2012
    In:  Nucleic Acids Research Vol. 40, No. 19 ( 2012-10), p. 9887-9896
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 40, No. 19 ( 2012-10), p. 9887-9896
    Type of Medium: Online Resource
    ISSN: 1362-4962 , 0305-1048
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2012
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 6
    In: Molecular Cell, Elsevier BV, Vol. 51, No. 2 ( 2013-07), p. 156-173
    Type of Medium: Online Resource
    ISSN: 1097-2765
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2013
    detail.hit.zdb_id: 2001948-8
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2013
    In:  Cancer Research Vol. 73, No. 8_Supplement ( 2013-04-15), p. 3202-3202
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 73, No. 8_Supplement ( 2013-04-15), p. 3202-3202
    Abstract: Glioblastoma multiforme (GBM) is the most common and malignant type of brain tumor in adults and is nearly uniformly fatal, with a median survival of one year. Diffuse infiltration, extensive neo-angiogenesis, uncontrolled cellular proliferation, presence of necrotic regions and resistance to apoptosis are all hallmark features of these tumors. The complex nature of GBMs is worsened by an incomplete understanding of its cellular origin and of the molecular determinants of its aggressiveness. This has contributed to make this cancer one of the most difficult to treat. Alternative splicing of pre-mRNA is an important mechanism to increase the diversity of protein functions; its dysregulation leads to the aberrant expression of specific protein isoforms, often associated with cancer. A relatively small number of splicing factors regulates the production of different splice variants of many proteins. In cancer, alterations in the expression of few splicing factors may lead to the aberrant splicing of several targets including oncogenes and tumor suppressors, which may contribute to the transformed cellular phenotype. Here, we investigate the tumorigenic role of the heterogeneous nuclear ribonucleoprotein PTBP1, a splicing factor commonly overexpressed in GBM. In the present study we used RNA immunoprecipitation and Exon Trap assay to describe how PTBP1 drives the aberrant splicing of a brain-specific exon in the membrane-binding tumor suppressor Annexin A7 (ANXA7). By differential overexpression of ANXA7 splice variants in tumor cell lines, we showed that expression of ANXA7 variant B, normally expressed in brain, controls EGFR pathway; conversely, the tumor variant ANXA7-vA does not stop EGFR activation cascade. Immunostaining experiments demonstrated that, compared to ANXA7-vB, ANXA7-vA reduces the endosomal targeting of EGFR and prolonging the activation of its signaling pathway. Knocking down PTBP1 in tumor cell lines restored the expression of ANXA7-vB and mimicked the effect of ANXA7-vB overexpression on EGFR trafficking and pathway activation. Furthermore, we performed in vivo experiments to show that PTBP1 increased expression has a general effect on tumor aggressiveness as it drives angiogenesis and promotes invasiveness. Finally, we assessed the association of PTBP1 expression and clinical outcome and we found that patients with high PTBP1 expression had a significantly worse survival rate. Our study highlights the important role the splicing factors play in cancer. In fact, the mechanism we describe here could represent a common paradigm of malignant transformation which could possibly lead to the development of new therapeutic strategies for GBM treatment. Citation Format: Roberto Ferrarese, Eva Bug, Daniel Maticzka, Wilfried Reichardt, Maria Stella Carro, Markus Bredel. PTBP1-mediated aberrant splicing of a brain-specific exon in ANXA7 promotes brain tumorigenesis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3202. doi:10.1158/1538-7445.AM2013-3202
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2013
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 8
    In: Nature, Springer Science and Business Media LLC, Vol. 544, No. 7648 ( 2017-4), p. 115-119
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
    RVK:
    RVK:
    RVK:
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 120714-3
    detail.hit.zdb_id: 1413423-8
    SSG: 11
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  • 9
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2020
    In:  Nucleic Acids Research Vol. 48, No. 3 ( 2020-02-20), p. e15-e15
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 48, No. 3 ( 2020-02-20), p. e15-e15
    Abstract: Determination of the in vivo binding sites of RNA-binding proteins (RBPs) is paramount to understanding their function and how they affect different aspects of gene regulation. With hundreds of RNA-binding proteins identified in human cells, a flexible, high-resolution, high-throughput, highly multiplexible and radioactivity-free method to determine their binding sites has not been described to date. Here we report FLASH (Fast Ligation of RNA after some sort of Affinity Purification for High-throughput Sequencing), which uses a special adapter design and an optimized protocol to determine protein–RNA interactions in living cells. The entire FLASH protocol, starting from cells on plates to a sequencing library, takes 1.5 days. We demonstrate the flexibility, speed and versatility of FLASH by using it to determine RNA targets of both tagged and endogenously expressed proteins under diverse conditions in vivo.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 10
    In: Blood, American Society of Hematology, Vol. 134, No. Supplement_1 ( 2019-11-13), p. 818-818
    Abstract: Hematopoietic stem cells (HSCs) are normally quiescent and have evolved mechanisms to respond to stress. Upon stress like chemotherapy, HSCs are activated, exit quiescence and differentiate to all hematopoietic lineages, features that are highly used in the clinic. Given the clinical relevance of HSCs, understanding the molecular mechanisms governing HSCs under homeostasis and regeneration is critical. Here we evaluated hematopoietic regeneration after chemotherapy using the myeloablative agent 5-fluorouracil (5-FU). We performed chromatin accessibility assays at steady state (D0), 16 hours (H16) and 3 days (D3) after treatment of wild type mice with 5-FU and observed that robust chromatin reorganisation takes place during the early time points of the response. Expression analysis at the same time points revealed that during regeneration, inflammatory signalling is activated. Surprisingly, we also detected increased transcription of repetitive elements (REs) during early recovery. Upregulated REs were located in genomic regions that gain accessibility during regeneration. We reasoned that newly transcribed REs could be responsible for the inflammatory signalling activation by acting as ligands for the innate immune receptor MDA5. Indeed, by sequencing the RNA that is crosslinked to MDA5 upon stress we found several RE transcripts bound to MDA5. Additionally, by performing digital footprinting analysis on our chromatin accessibility data we found increased occupancy of IRF and NF-κB motifs after chemotherapy. These data provided further indication that MDA5 is activated after chemotherapy since IRF and NF-κB factors act downstream of MDA5. We then investigated the role of MDA5 in HSC regeneration in vivo. Cell cycle analysis showed that Mda5-/- HSCs were more quiescent both at steady state and during regeneration. This quiescent phenotype was validated by metabolic assays and single-cell RNA-seq analysis. Due to their ability to retain quiescence, Mda5-/- HSCs harbour better repopulating capacity upon bone marrow transplantation, as higher chimerism was observed in secondary recipients when injected with Mda5-/- cells. In vitro serial Colony Forming Unit-Cell (CFU-C) of wild type and Mda5-/- HSCs or WT HSCs treated with TBK1 inhibitor, a kinase downstream of MDA5 and essential for signal mediation, verified our transplantation experiments. We reasoned that the quiescent phenotype of Mda5-/- HSCs could be due to the inability of Mda5-/- HSCs to upregulate either REs or inflammatory signaling upon regeneration. To answer this question we performed chromatin accessibility and expression assays in Mda5-/- HSCs at several time points after chemotherapy and compared them to wild type cells. Indeed, robust chromatin accessibility and upregulation of REs takes place in Mda5-/- HSCs but inflammatory signaling is impaired. Concomitantly we observed less phosho-IRF3 and less translocation of NF-κB to the nucleus in Mda5-/- HSCs thus verifying our expression analysis results. To prove that REs can indeed activate MDA5 leading to increased inflammatory signaling that facilitates HSCs to exit quiescence, we overexpressed two of these elements in wild type and Mda5-/- HSCs. Indeed overexpression of both elements in wild type HSCs led to enhanced exit from quiescence but this effect was abrogated in Mda5-/- HSCs. Our step-by-step model proposes that during regeneration, robust chromatin rearrangement and RE upregulation take place. Upregulated RE transcripts bind and activate the innate immune receptor MDA5 that in turn, stimulates the inflammatory signalling necessary for HSCs to exit quiescence and regenerate the hematopoietic system. Thus, using hematopoiesis as an exemplary system, our work uncovers a novel function of REs in tissue regeneration. Disclosures No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2019
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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