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TranscriptomicsComplexity of Murine Cardiomyocyte miRNA Biogenesis, Sequence Variant Expression and Function
microRNAs (miRNAs) are critical to heart development and disease. Emerging research indicates that regulated precursor processing can give rise to an unexpected diversity of miRNA variants. We subjected small RNA from murine HL-1 cardiomyocyte cells to next generation sequencing to investigate the r...
ORGANISM(S): Mus musculus 
2012-07-20 | E-GEOD-39531 | biostudies-arrayexpress
TranscriptomicsRe-evaluation of the roles of DROSHA, Exportin 5, and DICER in microRNA biogenesis
Biogenesis of canonical microRNAs (miRNAs) involves multiple steps: nuclear processing of primary miRNA (pri-miRNA) by DROSHA, nuclear export of precursor miRNA (pre-miRNA) by Exportin 5 (XPO5), and cytoplasmic processing of pre-miRNA by DICER. To gain a deeper understanding of the contribution of e...
ORGANISM(S): Homo sapiens 
2016-03-17 | E-GEOD-77989 | biostudies-arrayexpress
TranscriptomicsNOT2 proteins promote Pol II-dependent transcription and interact with multiple miRNA biogenesis factors in Arabidopsis
MicroRNAs (miRNAs) play key regulatory roles in numerous developmental and physiological processes in animals and plants. The elaborate mechanism of miRNA biogenesis involves transcription and multiple processing steps. Here, we report the identification of a pair of evolutionarily conserved NOT2_3_...
ORGANISM(S): Arabidopsis thaliana 
2013-01-30 | E-GEOD-42901 | biostudies-arrayexpress
TranscriptomicsA novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity
Here we identify a Dicer-independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 (Ago2). To uncover Dicer-independent miRNAs, we sequenced small RNAs in wild type, maternal-zygotic dicer (MZdicer) and MZago2 mutants, using zebrafish as a model system. We find t...
ORGANISM(S): Danio rerio 
2010-07-01 | E-GEOD-21503 | biostudies-arrayexpress
TranscriptomicsIn depth analysis of the interaction of HIV 1 with cellular microRNA biogenesis and effector mechanisms
The question of how HIV 1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4+ PBMCs and...
ORGANISM(S): Homo sapiens 
2014-07-31 | E-GEOD-59944 | biostudies-arrayexpress
TranscriptomicsIntertwined pathways for Argonaute-mediated microRNA biogenesis in Drosophila
Ago1-IP small RNA sequencing from S2R+ cells, with dsRNA knockdown of Dicer1 (and GFP control) One Dicer knockdown sample and one GFP knockdown control.
ORGANISM(S): Drosophila melanogaster 
2013-12-04 | E-GEOD-51585 | biostudies-arrayexpress
TranscriptomicsMultiple RNA recognition patterns during microRNA biogenesis in plants
MicroRNAs (miRNAs) are processed from longer precursors with fold-back structures. While animal MIRNA precursors have homogenous structures, plant precursors comprise a collection of fold-backs with variable size and shape. Here, we design an approach (SPARE) to systematically analyze miRNA processi...
ORGANISM(S): Arabidopsis thaliana 
2013-06-12 | E-GEOD-46429 | biostudies-arrayexpress
TranscriptomicsmRNA profiles following TUT knock-down in HeLa
The precise control of microRNA (miRNA) biogenesis is important for various cellular functions, and its dysregulation is often associated with human diseases. We previously reported that Terminal uridylyl transferase 4 (TUT4) down-regulates let-7 miRNA biogenesis by oligo-uridylating let-7 precur...
ORGANISM(S): Homo sapiens 
2012-10-16 | E-GEOD-40228 | biostudies-arrayexpress
TranscriptomicsRNA-seq of pooled Arabidopsis thaliana inflorescences of miRNA function related HWS overexpressors, mutants and transgenic lines
We wanted to characterize Arabidopsis HWS in the context of miRNA biogenesis and function. HWS mutant alleles were found to suppress the plant phenotype of a transgenic miRNA156 target mimicry line (MIM156) in a screen conducted in our lab. We analyzed gene expression of Arabidopsis wild-type plants...
ORGANISM(S): Arabidopsis thaliana 
2017-11-01 | E-MTAB-5788 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of mouse hearts from wild type and miRNA-1-2 knockout mutants at postnatal day 10 to provide insight into the role of miRNA-1-2 in cardiac development
Microarray was done on heart tissue from ko and wt; MicroRNAs (miRNAs) are genomically encoded small RNAs used by organisms to regulate the dosage of proteins generated from messenger RNA transcripts. The in vivo requirement of specific miRNAs in mammals is unknown, and reliable prediction of mRNA t...
ORGANISM(S): Mus musculus 
2007-12-12 | E-GEOD-7333 | biostudies-arrayexpress
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