Search publications
150 results for “genes”
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A role for alternative splicing in circadian control of exocytosis and glucose homeostasis.
Genes & development · 2020 · 34(15-16): 1089-1105
The circadian clock is encoded by a negative transcriptional feedback loop that coordinates physiology and behavior through molecular programs that remain incompletely understood. Here, we reveal rhythmic genome-wide alternative splicing (AS) of pre-mRNAs encoding regulators of peptidergic secretion within pancreatic …
PMID 32616519 DOI ↗
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A large-scale binding and functional map of human RNA-binding proteins.
Nature · 2020 · 583(7818): 711-719
Many proteins regulate the expression of genes by binding to specific regions encoded in the genome<sup>1</sup>. Here we introduce a new data set of RNA elements in the human genome that are recognized by RNA-binding proteins (RBPs), generated as part …
PMID 32728246 DOI ↗
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Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Nature · 2020 · 583(7818): 699-710
The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded …
PMID 32728249 DOI ↗
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Heterogenous Populations of Tissue-Resident CD8<sup>+</sup> T Cells Are Generated in Response to Infection and Malignancy.
Immunity · 2020 · 52(5): 808-824.e7
Tissue-resident memory CD8<sup>+</sup> T cells (Trm) provide host protection through continuous surveillance of non-lymphoid tissues. Using single-cell RNA-sequencing (scRNA-seq) and genetic reporter mice, we identified discrete lineages of intestinal antigen-specific CD8<sup>+</sup> T cells, including a Blimp1<sup>hi</sup>Id3<sup>lo</sup> tissue-resident effector cell population …
PMID 32433949 DOI ↗
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Early precursors and molecular determinants of tissue-resident memory CD8<sup>+</sup> T lymphocytes revealed by single-cell RNA sequencing.
Science immunology · 2020 · 5(47)
During an immune response to microbial infection, CD8<sup>+</sup> T cells give rise to distinct classes of cellular progeny that coordinately mediate clearance of the pathogen and provide long-lasting protection against reinfection, including a subset of noncirculating tissue-resident memory (T<sub>RM</sub>) cells …
PMID 32414833 DOI ↗
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The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.
Cell stem cell · 2019 · 25(5): 622-638.e13
Post-transcriptional mechanisms have the potential to influence complex changes in gene expression, yet their role in cell fate transitions remains largely unexplored. Here, we show that suppression of the RNA helicase DDX6 endows human and mouse primed embryonic stem cells …
PMID 31588046 DOI ↗
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Peptide Brush Polymers for Efficient Delivery of a Gene Editing Protein to Stem Cells.
Angewandte Chemie (International ed. in English) · 2019 · 58(44): 15646-15649
The scarcity of effective means to deliver functional proteins to living cells is a central problem in biotechnology and medicine. Herein, we report the efficient delivery of an active DNA-modifying enzyme to human stem cells through high-density cell penetrating peptide …
PMID 31404473 DOI ↗
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Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription.
Cell · 2019 · 178(1): 107-121.e18
Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA-binding proteins (RBPs). Although multiple RBPs have been implicated in transcription control, it has remained unclear how extensively RBPs directly act on …
PMID 31251911 DOI ↗
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Disruption in A-to-I Editing Levels Affects C. elegans Development More Than a Complete Lack of Editing.
Cell reports · 2019 · 27(4): 1244-1253.e4
A-to-I RNA editing, catalyzed by ADAR proteins, is widespread in eukaryotic transcriptomes. Studies showed that, in C. elegans, ADR-2 can actively deaminate dsRNA, whereas ADR-1 cannot. Therefore, we set out to study the effect of each of the ADAR genes …
PMID 31018137 DOI ↗
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RBP-Maps enables robust generation of splicing regulatory maps.
RNA (New York, N.Y.) · 2019 · 25(2): 193-204
Alternative splicing of pre-messenger RNA transcripts enables the generation of multiple protein isoforms from the same gene locus, providing a major source of protein diversity in mammalian genomes. RNA binding proteins (RBPs) bind to RNA to control splice site choice …
PMID 30413564 DOI ↗
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Overriding FUS autoregulation in mice triggers gain-of-toxic dysfunctions in RNA metabolism and autophagy-lysosome axis.
eLife · 2019 · 8
Mutations in coding and non-coding regions of FUS cause amyotrophic lateral sclerosis (ALS). The latter mutations may exert toxicity by increasing FUS accumulation. We show here that broad expression within the nervous system of wild-type or either of two ALS-linked …
PMID 30747709 DOI ↗
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Widespread RNA editing dysregulation in brains from autistic individuals.
Nature neuroscience · 2019 · 22(1): 25-36
Transcriptomic analyses of postmortem brains have begun to elucidate molecular abnormalities in autism spectrum disorder (ASD). However, a crucial pathway involved in synaptic development, RNA editing, has not yet been studied on a genome-wide scale. Here we profiled global patterns …
PMID 30559470 DOI ↗
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A Transcriptome-wide Translational Program Defined by LIN28B Expression Level.
Molecular cell · 2019 · 73(2): 304-313.e3
LIN28 RNA binding proteins are dynamically expressed throughout mammalian development and during disease. However, it remains unclear how changes in LIN28 expression define patterns of post-transcriptional gene regulation. Here we show that LIN28 expression level is a key variable that …
PMID 30527666 DOI ↗
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Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells.
Frontiers in molecular neuroscience · 2018 · 11: 261
The human brain is composed of a complex assembly of about 171 billion heterogeneous cellular units (86 billion neurons and 85 billion non-neuronal glia cells). A comprehensive description of brain cells is necessary to understand the nervous system in health …
PMID 30147644 DOI ↗
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An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys.
RNA (New York, N.Y.) · 2018 · 24(9): 1255-1265
During terminal erythropoiesis, the splicing machinery in differentiating erythroblasts executes a robust intron retention (IR) program that impacts expression of hundreds of genes. We studied IR mechanisms in the <i>SF3B1</i> splicing factor gene, which expresses ∼50% of its transcripts in …
PMID 29959282 DOI ↗
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Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS.
Acta neuropathologica · 2018 · 136(3): 405-423
Sporadic amyotrophic lateral sclerosis (sALS) is the most common form of ALS, however, the molecular mechanisms underlying cellular damage and motor neuron degeneration remain elusive. To identify molecular signatures of sALS we performed genome-wide expression profiling in laser capture microdissection-enriched …
PMID 29881994 DOI ↗
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Short poly(A) tails are a conserved feature of highly expressed genes.
Nature structural & molecular biology · 2017 · 24(12): 1057-1063
Poly(A) tails are important elements in mRNA translation and stability, although recent genome-wide studies have concluded that poly(A) tail length is generally not associated with translational efficiency in nonembryonic cells. To investigate whether poly(A) tail size might be coupled to …
PMID 29106412 DOI ↗
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Genetic mutations in RNA-binding proteins and their roles in ALS.
Human genetics · 2017 · 136(9): 1193-1214
Mutations in genes that encode RNA-binding proteins (RBPs) have emerged as critical determinants of neurological diseases, especially motor neuron disorders such as amyotrophic lateral sclerosis (ALS). RBPs are involved in all aspects of RNA processing, controlling the life cycle of …
PMID 28762175 DOI ↗
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The <i>C. elegans</i> neural editome reveals an ADAR target mRNA required for proper chemotaxis.
eLife · 2017 · 6
ADAR proteins alter gene expression both by catalyzing adenosine (A) to inosine (I) RNA editing and binding to regulatory elements in target RNAs. Loss of ADARs affects neuronal function in all animals studied to date. <i>Caenorhabditis elegans</i> lacking ADARs exhibit …
PMID 28925356 DOI ↗
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Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation.
Molecular cell · 2017 · 67(1): 148-161.e5
Alternative splicing (AS) generates isoform diversity for cellular identity and homeostasis in multicellular life. Although AS variation has been observed among single cells, little is known about the biological or evolutionary significance of such variation. We developed Expedition, a computational …
PMID 28673540 DOI ↗
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Pseudotemporal Ordering of Single Cells Reveals Metabolic Control of Postnatal β Cell Proliferation.
Cell metabolism · 2017 · 25(5): 1160-1175.e11
Pancreatic β cell mass for appropriate blood glucose control is established during early postnatal life. β cell proliferative capacity declines postnatally, but the extrinsic cues and intracellular signals that cause this decline remain unknown. To obtain a high-resolution map of …
PMID 28467932 DOI ↗
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Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer.
Cancer discovery · 2017 · 7(4): 410-423
Recent studies have characterized the extensive somatic alterations that arise during cancer. However, the somatic evolution of a tumor may be significantly affected by inherited polymorphisms carried in the germline. Here, we analyze genomic data for 5,954 tumors to reveal …
PMID 28188128 DOI ↗
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High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells.
Stem cell reports · 2017 · 8(4): 1101-1111
Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) offers the possibility of studying the molecular mechanisms underlying human diseases in cell types difficult to extract from living patients, such as neurons and cardiomyocytes. To date, studies have been published …
PMID 28410643 DOI ↗
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iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.
Stem cell reports · 2017 · 8(4): 1086-1100
Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 …
PMID 28410642 DOI ↗
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RNA-binding protein CPEB1 remodels host and viral RNA landscapes.
Nature structural & molecular biology · 2016 · 23(12): 1101-1110
Host and virus interactions occurring at the post-transcriptional level are critical for infection but remain poorly understood. Here, we performed comprehensive transcriptome-wide analyses revealing that human cytomegalovirus (HCMV) infection results in widespread alternative splicing (AS), shortening of 3' untranslated regions …
PMID 27775709 DOI ↗
Datasets 25+
Zfp697/ZNF697 is an RNA-binding protein that modulates TGF-β1 2 signaling and hepatic inflammation in liver disease
Mus musculus · GPL30172
Investigating m6A-relevant gene function in neural progenitor cells using CRISPR-Cas9 genome editing and RNA-seq
Homo sapiens · GPL24676
Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (eCLIP).
Homo sapiens · GPL24676
Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (RNA-Seq).
Homo sapiens · Illumina
Multi-Modal Comparison of human Hepatic Stellate Cells identifies novel therapeutic targets for Metabolic Dysfunction-Associated Steatotic Liver Disease
Homo sapiens · GPL24676, GPL37309
Ythdf m6A readers compensate each other in a context dependent manner [eCLIP]
GPL17021
Ythdf m6A readers compensate each other in a context dependent manner [Ribo-seq]
GPL21626
Ythdf m6A readers compensate each other in a context dependent manner [3'UTR RNA-seq]
GPL13112
Ythdf m6A readers compensate each other in a context dependent manner [RNA-seq]
GPL21626
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy
GPL24676
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [scRNA-Seq]
GPL24676
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [eCLIP]
GPL24676
Single-cell and isoform-specific translational profiling of the mouse brain with long-read sequencing [scRNA-Seq, longread]
GPL34585
Single-cell and isoform-specific translational profiling of the mouse brain [scRNA-seq]
GPL34475
Single cell and isoform-specific translational profiling of the mouse brain [ribostamp]
GPL24247
Single cell and isoform-specific translational profiling of the mouse brain [Bulk RNA-seq]
GPL24247
Single cell and isoform-specific translational profiling of the mouse brain [Ribo-STAMP]
GPL24247
Densely interconnected transcriptional circuits control cell states in human hematopoiesis
Homo sapiens · GPL4685
Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved insulin secretion by pancreatic β cells
Mus musculus · GPL13112
Disruption of human-specific synaptogenesis program in autism [RNA-seq]
9598 · GPL11154
Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation
9544 · GPL11154
Showing first 25 dataset results.
Analyses 25+
GSE315026 · 2 steps · eCLIP · geo_data_processing
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy. (2026)
GSE315443 · 2 steps · scRNA-seq · geo_data_processing
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy. (2026)
GSE317529 · 2 steps · eCLIP · geo_data_processing
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy. (2026)
GSE278725 · 9 steps · eCLIP · geo_data_processing
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis. (2025)
GSE279064 · 3 steps · eCLIP · geo_data_processing
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis. (2025)
GSE279065 · 9 steps · eCLIP · geo_data_processing
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis. (2025)
GSE123881 · 3 steps · RNA-Seq · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE124023 · 22 steps · RIP-Seq · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE13067 · 3 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE14333 · 2 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE145430 · 2 steps · RNA-Seq · code_examples
Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program. (2020)
GSE145984 · 5 steps · RNA-Seq · code_examples
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression. (2020)
GSE146726 · 4 steps · RNA-Seq · code_examples
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression. (2020)
GSE17536 · 3 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE17538 · 3 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE31595 · 2 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE33113 · 1 step · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE37892 · 3 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE46240 · 5 steps · RNA-Seq · code_examples
Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program. (2020)
GSE5851 · 1 step · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE87211 · 1 step · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE107766 · 33 steps · OTHER · code_examples
A protein-RNA interaction atlas of the ribosome biogenesis factor AATF. (2019)
GSE107767 · 33 steps · OTHER · code_examples
A protein-RNA interaction atlas of the ribosome biogenesis factor AATF. (2019)
GSE107768 · 33 steps · GSE · code_examples
A protein-RNA interaction atlas of the ribosome biogenesis factor AATF. (2019)
GSE59288 · 3 steps · RNA-Seq · code_examples
Widespread RNA editing dysregulation in brains from autistic individuals. (2019)
Showing first 25 analysis results.