Search publications
88 results for “genomics”
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Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for ALS and frontotemporal degeneration.
Proceedings of the National Academy of Sciences of the United States of America · 2013 · 110(47): E4530-9
Expanded hexanucleotide repeats in the chromosome 9 open reading frame 72 (C9orf72) gene are the most common genetic cause of ALS and frontotemporal degeneration (FTD). Here, we identify nuclear RNA foci containing the hexanucleotide expansion (GGGGCC) in patient cells, including …
PMID 24170860 DOI ↗
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Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing.
Molecular cell · 2013 · 50(2): 223-35
SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. …
PMID 23562324 DOI ↗
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Genome-wide approaches to dissect the roles of RNA binding proteins in translational control: implications for neurological diseases.
Frontiers in neuroscience · 2012 · 6: 144
Translational control of messenger RNAs (mRNAs) is a key aspect of neurobiology, defects of which can lead to neurological diseases. In response to stimuli, local translation of mRNAs is activated at synapses to facilitate long-lasting forms of synaptic plasticity, the …
PMID 23060744 DOI ↗
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Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration.
Development, growth & differentiation · 2012 · 54(7): 673-85
Salamanders possess an extraordinary capacity for tissue and organ regeneration when compared to mammals. In our effort to characterize the unique transcriptional fingerprint emerging during the early phase of salamander limb regeneration, we identified transcriptional activation of some germline-specific genes …
PMID 22913491 DOI ↗
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Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins.
Cell reports · 2012 · 1(2): 167-78
Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here, we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate …
PMID 22574288 DOI ↗
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Genome-wide approaches in the study of microRNA biology.
Wiley interdisciplinary reviews. Systems biology and medicine · 2011 · 3(5): 491-512
MicroRNAs (miRNAs), a class of ∼21-23 nucleotide long non-coding RNAs (ncRNAs), have critical roles in diverse biological processes that encompass development, proliferation, apoptosis, stress response, and fat metabolism. miRNAs recognize their target mRNA transcripts by partial sequence complementarity and collectively …
PMID 21197653 DOI ↗
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Alternative splicing in stem cell self-renewal and diferentiation.
Advances in experimental medicine and biology · 2010 · 695: 92-104
This chapter provides a review of recent advances in understanding the importance of alternative pre-messenger RNA splicing in stem cell biology. The majority of transcribed pre-mRNAs undergo RNA splicing where introns are excised and exons are juxtaposed to form mature …
PMID 21222201 DOI ↗
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Transcriptional signature and memory retention of human-induced pluripotent stem cells.
PloS one · 2009 · 4(9): e7076
Genetic reprogramming of somatic cells to a pluripotent state (induced pluripotent stem cells or iPSCs) by over-expression of specific genes has been accomplished using mouse and human cells. However, it is still unclear how similar human iPSCs are to human …
PMID 19763270 DOI ↗
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L1 retrotransposition in human neural progenitor cells.
Nature · 2009 · 460(7259): 1127-31
Long interspersed element 1 (LINE-1 or L1) retrotransposons have markedly affected the human genome. L1s must retrotranspose in the germ line or during early development to ensure their evolutionary success, yet the extent to which this process affects somatic cells …
PMID 19657334 DOI ↗
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The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians.
RNA (New York, N.Y.) · 2008 · 14(6): 1174-86
PIWI proteins are expressed in germ cells in a wide variety of metazoans, where they participate in the synthesis and function of a novel class of small RNAs called PIWI associated RNAs (piRNAs). One function of piRNAs is to preserve …
PMID 18456843 DOI ↗
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Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements.
PLoS genetics · 2007 · 3(5): e85
Knowledge of the functional cis-regulatory elements that regulate constitutive and alternative pre-mRNA splicing is fundamental for biology and medicine. Here we undertook a genome-wide comparative genomics approach using available mammalian genomes to identify conserved intronic splicing regulatory elements (ISREs). Our …
PMID 17530930 DOI ↗
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Splicing regulators: targets and drugs.
Genome biology · 2005 · 6(12): 240
Silencing of splicing regulators by RNA interference, combined with splicing-specific microarrays, has revealed a complex network of distinct alternative splicing events in Drosophila, while a high-throughput screen of more than 6,000 compounds has identified drugs that interfere specifically and directly …
PMID 16356274 DOI ↗
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Identification and analysis of alternative splicing events conserved in human and mouse.
Proceedings of the National Academy of Sciences of the United States of America · 2005 · 102(8): 2850-5
Alternative pre-mRNA splicing affects a majority of human genes and plays important roles in development and disease. Alternative splicing (AS) events conserved since the divergence of human and mouse are likely of primary biological importance, but relatively few of such …
PMID 15708978 DOI ↗
Datasets 11
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [scRNA-Seq]
GPL24676
Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner
GPL24247
Phase II exploratory pharmacogenomics study of cetuximab monotherapy in patients with advanced metastatic CRC
Homo sapiens · GPL571
Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients (Moffitt Samples)
Homo sapiens · GPL570
A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Mount Sinai Hospital (MSH) Population Specimen Collection and Profiling of Inflammatory Bowel Disease
Homo sapiens · GPL16791
Sporadic ALS has compartment-specific aberrant exon splicing and altered cell-matrix adhesion biology
Homo sapiens · GPL5188
Single-cell transcriptomics analysis of pancreatic primary tumor and metastatic biopsy tissues
Homo sapiens · GPL20301
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]
Homo sapiens · GPL24676
Whole brain RNA from congenic littermates does not support a general effect of Nxf1 CAST alleles on alternative pre-mRNA processing
Mus musculus · GPL13185
Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (Affymetrix)
Mus musculus · GPL13185
Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (microarray)
Mus musculus · GPL13185
Analyses 2
GSE83687 · 4 steps · RNA-Seq · code_examples
RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine. (2022)
GSE5851 · 1 step · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)