MiRNA expression in granulopoiesis
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE21437 | GEO | 2010/04/22
SECONDARY ACCESSION(S): PRJNA126349
REPOSITORIES: GEO
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Project description:Normal human neutrophil development is a complex biological process, where the balance between cell proliferation, differentiation and apoptosis is tightly regulated by a transcriptional program that results in the production of appropriate numbers of circulating mature neutrophils. MicroRNAs (miRNAs) are small non-coding RNAs of 18~25 nt that affect cellular protein levels. Only limited data is available on miRNA expression patterns during normal granulocytic differentiation of primary human cells. We have examined miRNA expression patterns in distinct stages of granulocytic differentiation sorted from human bone marrow and identified highly stage-specific expressed miRNAs. Some of these differentially expressed miRNA are related to each other in terms of seed sequence (miRNA families) and location on the genome (miRNA clusters). These data reveal distinct expression patterns of specific miRNA sets that closely follow the transition of discrete maturation stages along the myeloblast-neutrophil pathway. In total 13 samples were measured, 2 myeloblast, 3 myeloblast/promyelocyte, 4 metamyelocytes and 3 neutrophils
2010-04-22 | E-GEOD-21437 | biostudies-arrayexpress
Project description:The aim of this study was to characterize in vivo miRNA expression in normal myeloid development of the neutrophil granulocyte (granulopoiesis) to gain insight into miRNA control of these processes. Cell populations highly enriched in precursors from successive stages of granulopoiesis and mature neutrophils were isolated from bone marrow (BM) and peripheral blood (PB) samples, respectively, from 4 healthy human donors. Total RNA was extracted from each cell population and subjected to miRNA gene expression profiling using miRCURYTM LNA microRNA Arrays Total RNA from cell populations highly enriched in precursors from three succesive stages of neutrophil granulopoiesis and mature neutrophils isolated from bone marrow and peripheral blood, respectively, from four healthy donors (SKP, AJ, AO, JO). The three cell populations from bone marrow where extracted and named B3, B2, and B1, corresponding to immature (myeloblasts [MBs] and promyelocytes [PMs]); intermediate mature (myelocytes [MCs] and metamyelocytes [MMs]); and mature neutrophil cells (band cells [BCs] and segmented neutrophil cells [SCs]), respectively, as described in Bjerregaard MD, Jurlander J, Klausen P, Borregaard N, Cowland JB: The in vivo profile of transcription factors during neutrophil differentiation in human bone marrow. Blood 2003, 101: 4322-4332. In total, 16 samples were compared (4 cell maturation stages from 4 donors)
2011-10-21 | E-GEOD-33140 | biostudies-arrayexpress
Project description:Schmitz2014 - RNA triplex formation
The model is parameterized using the
parameters for gene CCDC3 from Supplementary Table S1. The two
miRNAs which form the triplex together with CCDC3 are miR-551b and
miR-138.
This model is described in the article:
Cooperative gene regulation
by microRNA pairs and their identification using a
computational workflow.
Schmitz U, Lai X, Winter F,
Wolkenhauer O, Vera J, Gupta SK.
Nucleic Acids Res. 2014 Jul; 42(12):
7539-7552
Abstract:
MicroRNAs (miRNAs) are an integral part of gene regulation
at the post-transcriptional level. Recently, it has been shown
that pairs of miRNAs can repress the translation of a target
mRNA in a cooperative manner, which leads to an enhanced
effectiveness and specificity in target repression. However, it
remains unclear which miRNA pairs can synergize and which genes
are target of cooperative miRNA regulation. In this paper, we
present a computational workflow for the prediction and
analysis of cooperating miRNAs and their mutual target genes,
which we refer to as RNA triplexes. The workflow integrates
methods of miRNA target prediction; triplex structure analysis;
molecular dynamics simulations and mathematical modeling for a
reliable prediction of functional RNA triplexes and target
repression efficiency. In a case study we analyzed the human
genome and identified several thousand targets of cooperative
gene regulation. Our results suggest that miRNA cooperativity
is a frequent mechanism for an enhanced target repression by
pairs of miRNAs facilitating distinctive and fine-tuned target
gene expression patterns. Human RNA triplexes predicted and
characterized in this study are organized in a web resource at
www.sbi.uni-rostock.de/triplexrna/.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000530.
To cite BioModels Database, please use:
BioModels Database:
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To the extent possible under law, all copyright and related or
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2013-10-23 | BIOMD0000000530 | BioModels
Project description:Gene expression of human bone marrow granulocytic differentiation stages
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