In vivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs

<p>Abstract</p> <p>Background</p> <p>Noncoding RNAs (ncRNAs) play important roles in a variety of cellular processes. Characterizing the transcriptional activity of ncRNA promoters is therefore a critical step toward understanding the complex cellular roles of ncRNAs.</p> <p>Results</p> <p>Here we present an <it>in vivo </it>transcriptional analysis of three <it>C. elegans </it>ncRNA upstream motifs (UM1-3). Transcriptional activity of all three motifs has been demonstrated, and mutational analysis revealed differential contributions of different parts of each motif. We showed that upstream motif 1 (UM1) can drive the expression of green fluorescent protein (GFP), and utilized this for detailed analysis of temporal and spatial expression patterns of 5 SL2 RNAs. Upstream motifs 2 and 3 do not drive GFP expression, and termination at consecutive T runs suggests transcription by RNA polymerase III. The UM2 sequence resembles the tRNA promoter, and is actually embedded within its own short-lived, primary transcript. This is a structure which is also found at a few plant and yeast loci, and may indicate an evolutionarily very old dicistronic transcription pattern in which a tRNA serves as a promoter for an adjacent snoRNA.</p> <p>Conclusion</p> <p>The study has demonstrated that the three upstream motifs UM1-3 have promoter activity. The UM1 sequence can drive expression of GFP, which allows for the use of UM1::GFP fusion constructs to study temporal-spatial expression patterns of UM1 ncRNA loci. The UM1 loci appear to act in concert with other upstream sequences, whereas the transcriptional activities of the UM2 and UM3 are confined to the motifs themselves.</p

MicroRNA-encoding long non-coding RNAs

© 2008 He et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Analisis Kesalahan Penggunaan Ejaan Pada Skripsi Mahasiswa Program Studi Di Pendidikan Guru Sekolah Dasarfakultas Keguruan Dan Ilmu Pendidikan Universitas Darul Ulum Islamic Centre Sudirman Guppi Undaris

Penelitian ini bertujuan untuk mendeskripsikan kesalahan pemakaian huruf pada skripsi mahasiswa PGSD UNDARIS, medeskripsikan kesalahan penulisan kata pada skripsi mahasiswa PGSD UNDARIS, medeskripsikan kesalahan penulisan unsur serapan pada skripsi mahasiswa PGSD UNDARIS, dan medeskripsikan kesalahan penulisan tanda baca pada skripsi mahasiswa PGSD UNDARIS. Subjek penelitian ini adalah hasil penelitian pada skripsi mahasiswa PGSD UNDARIS.Jumlah skripsi yang dianalisis berjumlah 4 skripsi mahasiswa PGSD UNDARIS.Teknik pengumpulan data dalam penelitian ini menggunakan teknik baca.Teknik baca yang dilakukan adalah membaca secara berulang dan cermat skripsi mahasiswa PGSD UNDARIS yang telah dipilih.Sebelum dilakukan pencatatan, terlebih dahulu dilakukan pencatatan data pada kartu data, kemudian kartu data tersebut dikategorikan menurut kriteria kesalahan ejaan.Data yang terkumpul, kemudian dianalisis dan dideskripsikan.Instrumen pengumpulan data ini adalah menggunakan human instrument yaitu peneliti sendiri. Peneliti sebagai pelaksana yang akan mengumpulkan data, menganalisis, dan sekaligus membuat simpulan. Hasil penelitian ini menunjukkan bahwa kesalahan ejaan pada skripsi mahasiswa prodi PGSD Universitas Darul Ulum Islamic Centre Sudirman GUPPI sebanyak 247 kesalahan yang terdiri : (1) kesalahan pemakaian huruf kapital sebanyak 8 kesalahan, (2) kesalahan penulisan kata depan di dan ke sebanyak 30 kesalahan, yang meliputi kesalahan penulisan kata depan disebanyak 28 kesalahan, kesalahan penulisan kata depan ke sebanyak 2 kesalahan, sedangkan i mbuhan di-, ke-, dan kata depan dari tidak ditemukan kesalahan pada skripsi mahasiswa, (3) kesalahan pemakaian tanda baca sebanyak 209 kesalahan, yang meliputi kesalahan pemakaian tanda baca titik (.) sebanyak 34 kesalahan, kesalahan pemakaian tanda baca koma (,) sebanyak 163 kesalahan, kesalahan pemakaian tanda hubung (-) sebanyak 1 kesalahan, kesalahan pemakaian tanda tanya (?) sebanyak 4 kesalahan, dan kesalahan pemakaian tanda baca titik dua (:) sebanyak 8 kesalahan, dan (4) kesalahan pemakaian tanda seru (!), kesalahan pemakaian tanda baca titik koma (;), kesalahan pemakaian tanda petik tunggal (‘ ...\u27), kesalahan pemakaian tanda petik (“...”), dan kesalahan pemakaian tanda garis miring (/) tidak ditemukan kesalahan

Analysis of optimized DNase-seq reveals intrinsic bias in transcription factor footprint identification

DNase-seq is a powerful technique for identifying cis-regulatory elements across the genome. We studied the key experimental parameters to optimize the performance of DNase-seq. We found that sequencing short 50-100bp fragments that accumulate in long inter-nucleosome linker regions is more efficient for identifying transcription factor binding sites than using longer fragments. We also assessed the potential of DNase-seq to predict transcription factor occupancy through the generation of nucleotide-resolution transcription factor footprints. In modeling the sequence-specific DNaseI cutting bias we found a surprisingly strong effect that varied over more than two orders of magnitude. This confounds DNaseI footprint analysis to the extent that the nucleotide resolution cleavage patterns at most transcription factor binding sites are derived from intrinsic DNaseI cleavage bias rather than from specific protein-DNA interactions. In contrast, quantitative comparison of DNaseI hypersensitivity between states can predict transcription factor occupancy associated with particular biological perturbations

Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray

Small non-coding RNAs (ncRNAs) are encoded by genes that function at the RNA level, and several hundred ncRNAs have been identified in various organisms. Here we describe an analysis of the small non-coding transcriptome of Caenorhabditis elegans, microRNAs excepted. As a substantial fraction of the ncRNAs is located in introns of protein-coding genes in C.elegans, we also analysed the relationship between ncRNA and host gene expression. To this end, we designed a combined microarray, which included probes against ncRNA as well as host gene mRNA transcripts. The microarray revealed pronounced differences in expression profiles, even among ncRNAs with housekeeping functions (e.g. snRNAs and snoRNAs), indicating distinct developmental regulation and stage-specific functions of a number of novel transcripts. Analysis of ncRNA–host mRNA relations showed that the expression of intronic ncRNA loci with conserved upstream motifs was not correlated to (and much higher than) expression levels of their host genes. Even promoter-less intronic ncRNA loci, though showing a clear correlation to host gene expression, appeared to have a surprising amount of ‘expressional freedom’, depending on host gene function. Taken together, our microarray analysis presents a more complete and detailed picture of a non-coding transcriptome than hitherto has been presented for any other multicellular organism

Digital Quantification of Gene Expression in Sequential Breast Cancer Biopsies Reveals Activation of an Immune Response

Advancements in molecular biology have unveiled multiple breast cancer promoting pathways and potential therapeutic targets. Large randomized clinical trials remain the ultimate means of validating therapeutic efficacy, but they require large cohorts of patients and are lengthy and costly. A useful approach is to conduct a window of opportunity study in which patients are exposed to a drug pre-surgically during the interval between the core needle biopsy and the definitive surgery. These are non-therapeutic studies and the end point is not clinical or pathological response but rather evaluation of molecular changes in the tumor specimens that can predict response. However, since the end points of the non-therapeutic studies are biologic, it is critical to first define the biologic changes that occur in the absence of treatment. In this study, we compared the molecular profiles of breast cancer tumors at the time of the diagnostic biopsy versus the definitive surgery in the absence of any intervention using the Nanostring nCounter platform. We found that while the majority of the transcripts did not vary between the two biopsies, there was evidence of activation of immune related genes in response to the first biopsy and further investigations of the immune changes after a biopsy in early breast cancer seem warranted