Search Results - "Haberman, Nejc"

Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing by Attig, Jan, Agostini, Federico, Gooding, Clare, Chakrabarti, Anob M., Singh, Aarti, Haberman, Nejc, Zagalak, Julian A., Emmett, Warren, Smith, Christopher W.J., Luscombe, Nicholas M., Ule, Jernej

“…Long mammalian introns make it challenging for the RNA processing machinery to identify exons accurately. We find that LINE-derived sequences (LINEs)…”
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Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing by Blazquez, Lorea, Emmett, Warren, Faraway, Rupert, Pineda, Jose Mario Bello, Bajew, Simon, Gohr, Andre, Haberman, Nejc, Sibley, Christopher R, Bradley, Robert K, Irimia, Manuel, Ule, Jernej

“…Recursive splicing (RS) starts by defining an "RS-exon," which is then spliced to the preceding exon, thus creating a recursive 5' splice site (RS-5ss)…”
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The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila by Obrdlik, Ales, Lin, Gen, Haberman, Nejc, Ule, Jernej, Ephrussi, Anne

“…Exon junction complex (EJC) assembles after splicing at specific positions upstream of exon-exon junctions in mRNAs of all higher eukaryotes, affecting major…”
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A systems view of spliceosomal assembly and branchpoints with iCLIP by Briese, Michael, Haberman, Nejc, Sibley, Christopher R., Faraway, Rupert, Elser, Andrea S., Chakrabarti, Anob M., Wang, Zhen, König, Julian, Perera, David, Wickramasinghe, Vihandha O., Venkitaraman, Ashok R., Luscombe, Nicholas M., Saieva, Luciano, Pellizzoni, Livio, Smith, Christopher W. J., Curk, Tomaž, Ule, Jernej

“…Studies of spliceosomal interactions are challenging due to their dynamic nature. Here we used spliceosome iCLIP, which immunoprecipitates SmB along with small…”
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Splicing repression allows the gradual emergence of new Alu-exons in primate evolution by Attig, Jan, Ruiz de Los Mozos, Igor, Haberman, Nejc, Wang, Zhen, Emmett, Warren, Zarnack, Kathi, König, Julian, Ule, Jernej

“…Alu elements are retrotransposons that frequently form new exons during primate evolution. Here, we assess the interplay of splicing repression by hnRNPC and…”
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3′ UTR Length and Messenger Ribonucleoprotein Composition Determine Endocleavage Efficiencies at Termination Codons by Boehm, Volker, Haberman, Nejc, Ottens, Franziska, Ule, Jernej, Gehring, Niels H.

“…Nonsense-mediated mRNA decay (NMD) degrades different classes of mRNAs, including transcripts with premature termination codons (PTCs). The NMD factor SMG6…”
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High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43 by Rot, Gregor, Wang, Zhen, Huppertz, Ina, Modic, Miha, Lenče, Tina, Hallegger, Martina, Haberman, Nejc, Curk, Tomaž, von Mering, Christian, Ule, Jernej

“…Many RNA-binding proteins (RBPs) regulate both alternative exons and poly(A) site selection. To understand their regulatory principles, we…”
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Widespread 3′UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites by Haberman, Nejc, Digby, Holly, Faraway, Rupert, Cheung, Rebecca, Chakrabarti, Anob M., Jobbins, Andrew M., Parr, Callum, Yasuzawa, Kayoko, Kasukawa, Takeya, Yip, Chi Wai, Kato, Masaki, Takahashi, Hazuki, Carninci, Piero, Vernia, Santiago, Ule, Jernej, Sibley, Christopher R., Martinez-Sanchez, Aida, Lenhard, Boris

“…Abstract The 3′ untranslated region (3′UTR) plays a crucial role in determining mRNA stability, localisation, translation and degradation. Cap analysis of gene…”
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Publisher Correction: A systems view of spliceosomal assembly and branchpoints with iCLIP by Briese, Michael, Haberman, Nejc, Sibley, Christopher R., Faraway, Rupert, Elser, Andrea S., Chakrabarti, Anob M., Wang, Zhen, König, Julian, Perera, David, Wickramasinghe, Vihandha O., Venkitaraman, Ashok R., Luscombe, Nicholas M., Saieva, Luciano, Pellizzoni, Livio, Smith, Christopher W. J., Curk, Tomaž, Ule, Jernej

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Author Correction: A systems view of spliceosomal assembly and branchpoints with iCLIP by Briese, Michael, Haberman, Nejc, Sibley, Christopher R., Faraway, Rupert, Elser, Andrea S., Chakrabarti, Anob M., Wang, Zhen, König, Julian, Perera, David, Wickramasinghe, Vihandha O., Venkitaraman, Ashok R., Luscombe, Nicholas M., Saieva, Luciano, Pellizzoni, Livio, Smith, Christopher W. J., Curk, Tomaž, Ule, Jernej

“…An amendment to this paper has been published and can be accessed via a link at the top of the paper…”
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Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain by Rogelj, Boris, Easton, Laura E., Bogu, Gireesh K., Stanton, Lawrence W., Rot, Gregor, Curk, Tomaž, Zupan, Blaž, Sugimoto, Yoichiro, Modic, Miha, Haberman, Nejc, Tollervey, James, Fujii, Ritsuko, Takumi, Toru, Shaw, Christopher E., Ule, Jernej

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Erratum to: Insights into the design and interpretation of iCLIP experiments by Haberman, Nejc, Huppertz, Ina, Attig, Jan, König, Julian, Wang, Zhen, Hauer, Christian, Hentze, Matthias W, Kulozik, Andreas E, Le Hir, Hervé, Curk, Tomaž, Sibley, Christopher R, Zarnack, Kathi, Ule, Jernej

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'Read-through marking' reveals differential nucleotide composition of read-through and truncated cDNAs in iCLIP by Huppertz, Ina, Haberman, Nejc, Ule, Jernej

“…We established a modified iCLIP protocol, called 'read-through marking', which facilitates the detection of cDNAs that have not been truncated upon…”
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Splicing of long non-coding RNAs primarily depends on polypyrimidine tract and 5′ splice-site sequences due to weak interactions with SR proteins by Krchňáková, Zuzana, Thakur, Prasoon Kumar, Krausová, Michaela, Bieberstein, Nicole, Haberman, Nejc, Müller-McNicoll, Michaela, Staněk, David

“…Abstract Many nascent long non-coding RNAs (lncRNAs) undergo the same maturation steps as pre-mRNAs of protein-coding genes (PCGs), but they are often poorly…”
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Liver kinase B1 (LKB1) regulates the epigenetic landscape of mouse pancreatic beta cells by Haberman, Nejc, Cheung, Rebecca, Pizza, Grazia, Cvetesic, Nevena, Nagy, Dorka, Maude, Hannah, Blazquez, Lorea, Lenhard, Boris, Cebola, Inês, Rutter, Guy A., Martinez‐Sanchez, Aida

“…Liver kinase B1 (LKB1/STK11) is an important regulator of pancreatic β‐cell identity and function. Elimination of Lkb1 from the β‐cell results in improved…”
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Recursive splicing in long vertebrate genes by Sibley, Christopher R., Emmett, Warren, Blazquez, Lorea, Faro, Ana, Haberman, Nejc, Briese, Michael, Trabzuni, Daniah, Ryten, Mina, Weale, Michael E., Hardy, John, Modic, Miha, Curk, Tomaž, Wilson, Stephen W., Plagnol, Vincent, Ule, Jernej

“…Highly conserved recursive splice sites are identified in vertebrates, particularly within long genes encoding proteins that are involved in neuronal…”
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Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain by Rogelj, Boris, Easton, Laura E., Bogu, Gireesh K., Stanton, Lawrence W., Rot, Gregor, Curk, Tomaž, Zupan, Blaž, Sugimoto, Yoichiro, Modic, Miha, Haberman, Nejc, Tollervey, James, Fujii, Ritsuko, Takumi, Toru, Shaw, Christopher E., Ule, Jernej

“…Fused in sarcoma (FUS) and TAR DNA-binding protein 43 (TDP-43) are RNA-binding proteins pathogenetically linked to amyotrophic lateral sclerosis (ALS) and…”
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Dysregulated RNA polyadenylation contributes to metabolic impairment in non-alcoholic fatty liver disease by Jobbins, Andrew M, Haberman, Nejc, Artigas, Natalia, Amourda, Christopher, Paterson, Helen A B, Yu, Sijia, Blackford, Samuel J I, Montoya, Alex, Dore, Marian, Wang, Yi-Fang, Sardini, Alessandro, Cebola, Inês, Zuber, Johannes, Rashid, Sheikh Tamir, Lenhard, Boris, Vernia, Santiago

“…Abstract Pre-mRNA processing is an essential mechanism for the generation of mature mRNA and the regulation of gene expression in eukaryotic cells. While…”
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Insights into the design and interpretation of iCLIP experiments by Haberman, Nejc, Huppertz, Ina, Attig, Jan, König, Julian, Wang, Zhen, Hauer, Christian, Hentze, Matthias W, Kulozik, Andreas E, Le Hir, Hervé, Curk, Tomaž, Sibley, Christopher R, Zarnack, Kathi, Ule, Jernej

“…Ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) identifies the sites on RNAs that are in direct contact with RNA-binding proteins (RBPs). Several…”
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Widespread 3'UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites by Haberman, Nejc, Digby, Holly, Faraway, Rupert, Cheung, Rebecca, Chakrabarti, Anob M, Jobbins, Andrew M, Parr, Callum, Yasuzawa, Kayoko, Kasukawa, Takeya, Yip, Chi Wai, Kato, Masaki, Takahashi, Hazuki, Carninci, Piero, Vernia, Santiago, Ule, Jernej, Sibley, Christopher R, Martinez-Sanchez, Aida, Lenhard, Boris

“…The 3' untranslated region (3'UTR) plays a crucial role in determining mRNA stability, localisation, translation and degradation. Cap analysis of gene…”
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