We are analyzing https://link.springer.com/article/10.1186/gb-2014-15-1-r8.

Title:
PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast | Genome Biology
Description:
Background Nrd1 and Nab3 are essential sequence-specific yeast RNA binding proteins that function as a heterodimer in the processing and degradation of diverse classes of RNAs. These proteins also regulate several mRNA coding genes; however, it remains unclear exactly what percentage of the mRNA component of the transcriptome these proteins control. To address this question, we used the pyCRAC software package developed in our laboratory to analyze CRAC and PAR-CLIP data for Nrd1-Nab3-RNA interactions. Results We generated high-resolution maps of Nrd1-Nab3-RNA interactions, from which we have uncovered hundreds of new Nrd1-Nab3 mRNA targets, representing between 20 and 30% of protein-coding transcripts. Although Nrd1 and Nab3 showed a preference for binding near 5′ ends of relatively short transcripts, they bound transcripts throughout coding sequences and 3′ UTRs. Moreover, our data for Nrd1-Nab3 binding to 3′ UTRs was consistent with a role for these proteins in the termination of transcription. Our data also support a tight integration of Nrd1-Nab3 with the nutrient response pathway. Finally, we provide experimental evidence for some of our predictions, using northern blot and RT-PCR assays. Conclusions Collectively, our data support the notion that Nrd1 and Nab3 function is tightly integrated with the nutrient response and indicate a role for these proteins in the regulation of many mRNA coding genes. Further, we provide evidence to support the hypothesis that Nrd1-Nab3 represents a failsafe termination mechanism in instances of readthrough transcription.
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Keywords {🔍}

nab, nrd, figure, motifs, data, transcription, transcripts, rna, article, genes, google, scholar, termination, nrdnab, binding, sites, crosslinked, mrna, analyses, gene, parclip, coding, yeast, proteins, number, sequences, levels, genome, protein, utrs, cell, genomic, distribution, file, read, coverage, downstream, ipp, mol, pycrac, polymerase, regions, yta, crosslinking, polyadenylation, analysis, generated, role, shown, expression,

Topics {✒️}

nrd1-nab3-sen1-dependent transcription termination /view/swebb/pycrac] fastx-toolkit uv-induced cross-linking sites nrd1-nab3-dependent premature termination nrd1-nab3-dependent transcription termination end-point rt-pcr reactions jp/~mdehoon/software/cluster/index nrd1-nab3-directed transcription termination nrd1-dependent transcription termination precede cpf-dependent termination gene transfer format cross-linked nrd1-nab3 motifs xrn1-sensitive antisense regulatory sample kolmogorov-smirnov test recent high-throughput studies xrn1-sensitive unstable transcript nuclear polyadenylated rna-binding uv cross-linked rnas xrn1-sensitive unstable transcripts fail-safe transcriptional termination transcriptome-wide binding sites au-rich sequences surrounding par-clip data overlapped mov10 par-clip data genome-wide chip data post-transcriptional rna processing nrd1-nab3-rna interactions high-throughput sequencing data contained cross-linked nrd1 end-point rt-pcr substantial nab3 cross-linking individual-nucleotide resolution clip rna polymerase ii saccharomyces genome database au-rich nrd1 motifs control par-clip samples wellcome trust research article number r8 article download pdf transcriptome search search par-clip analyses showed nab3 par-clip datasets /usr/local/bin/ directory org/sgrann/pycrac] porrua nab3 par-clip data generated high-resolution maps au-rich polyadenylation sequences nrd1-nab3 termination pathway nrd1 par-clip data cross-linked nrd1 motifs

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WebPage:
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         headline:PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast
         description:Nrd1 and Nab3 are essential sequence-specific yeast RNA binding proteins that function as a heterodimer in the processing and degradation of diverse classes of RNAs. These proteins also regulate several mRNA coding genes; however, it remains unclear exactly what percentage of the mRNA component of the transcriptome these proteins control. To address this question, we used the pyCRAC software package developed in our laboratory to analyze CRAC and PAR-CLIP data for Nrd1-Nab3-RNA interactions. We generated high-resolution maps of Nrd1-Nab3-RNA interactions, from which we have uncovered hundreds of new Nrd1-Nab3 mRNA targets, representing between 20 and 30% of protein-coding transcripts. Although Nrd1 and Nab3 showed a preference for binding near 5′ ends of relatively short transcripts, they bound transcripts throughout coding sequences and 3′ UTRs. Moreover, our data for Nrd1-Nab3 binding to 3′ UTRs was consistent with a role for these proteins in the termination of transcription. Our data also support a tight integration of Nrd1-Nab3 with the nutrient response pathway. Finally, we provide experimental evidence for some of our predictions, using northern blot and RT-PCR assays. Collectively, our data support the notion that Nrd1 and Nab3 function is tightly integrated with the nutrient response and indicate a role for these proteins in the regulation of many mRNA coding genes. Further, we provide evidence to support the hypothesis that Nrd1-Nab3 represents a failsafe termination mechanism in instances of readthrough transcription.
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            Transcription Termination
            Saccharomyces Genome Database
            Alternative TSSs
            Gene Transfer Format
            Readthrough Transcription
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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      headline:PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast
      description:Nrd1 and Nab3 are essential sequence-specific yeast RNA binding proteins that function as a heterodimer in the processing and degradation of diverse classes of RNAs. These proteins also regulate several mRNA coding genes; however, it remains unclear exactly what percentage of the mRNA component of the transcriptome these proteins control. To address this question, we used the pyCRAC software package developed in our laboratory to analyze CRAC and PAR-CLIP data for Nrd1-Nab3-RNA interactions. We generated high-resolution maps of Nrd1-Nab3-RNA interactions, from which we have uncovered hundreds of new Nrd1-Nab3 mRNA targets, representing between 20 and 30% of protein-coding transcripts. Although Nrd1 and Nab3 showed a preference for binding near 5′ ends of relatively short transcripts, they bound transcripts throughout coding sequences and 3′ UTRs. Moreover, our data for Nrd1-Nab3 binding to 3′ UTRs was consistent with a role for these proteins in the termination of transcription. Our data also support a tight integration of Nrd1-Nab3 with the nutrient response pathway. Finally, we provide experimental evidence for some of our predictions, using northern blot and RT-PCR assays. Collectively, our data support the notion that Nrd1 and Nab3 function is tightly integrated with the nutrient response and indicate a role for these proteins in the regulation of many mRNA coding genes. Further, we provide evidence to support the hypothesis that Nrd1-Nab3 represents a failsafe termination mechanism in instances of readthrough transcription.
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         Transcription Termination
         Saccharomyces Genome Database
         Alternative TSSs
         Gene Transfer Format
         Readthrough Transcription
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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