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13 results for “chromatin”
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Human AUTS2 regulates neurodevelopmental pathways via dual DNA/RNA binding.
bioRxiv : the preprint server for biology · 2025
The <i>AUTS2</i> gene is implicated in neurodevelopmental and psychiatric disorders, with patient mutations leading to intellectual disability, microcephaly, and autistic behavior. While AUTS2's chromatin-and RNA-related functions are recognized, its direct binding to RNA in human neural progenitors has not been …
PMID 41278797 DOI ↗
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Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes.
Cell reports · 2024 · 43(8): 114637
Reactive changes of glial cells during neuroinflammation impact brain disorders and disease progression. Elucidating the mechanisms that control reactive gliosis may help us to understand brain pathophysiology and improve outcomes. Here, we report that adult ablation of autism spectrum disorder …
PMID 39154337 DOI ↗
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The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression.
The Journal of experimental medicine · 2022 · 219(6)
During an immune response to microbial infection, CD8+ T cells give rise to short-lived effector cells and memory cells that provide sustained protection. Although the transcriptional programs regulating CD8+ T cell differentiation have been extensively characterized, the role of long …
PMID 35593887 DOI ↗
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Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.
Molecular cell · 2022 · 82(3): 645-659.e9
Pseudouridine is a modified nucleotide that is prevalent in human mRNAs and is dynamically regulated. Here, we investigate when in their life cycle mRNAs become pseudouridylated to illuminate the potential regulatory functions of endogenous mRNA pseudouridylation. Using single-nucleotide resolution pseudouridine …
PMID 35051350 DOI ↗
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A multi-scale map of cell structure fusing protein images and interactions.
Nature · 2021 · 600(7889): 536-542
The cell is a multi-scale structure with modular organization across at least four orders of magnitude<sup>1</sup>. Two central approaches for mapping this structure-protein fluorescent imaging and protein biophysical association-each generate extensive datasets, but of distinct qualities and resolutions that are …
PMID 34819669 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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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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An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia.
Nature cancer · 2020 · 1(4): 410-422
Aggressive myeloid leukemias such as blast crisis chronic myeloid leukemia and acute myeloid leukemia remain highly lethal. Here we report a genome-wide in vivo CRISPR screen to identify new dependencies in this disease. Among these, RNA-binding proteins (RBPs) in general, …
PMID 34109316 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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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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A Small RNA-Catalytic Argonaute Pathway Tunes Germline Transcript Levels to Ensure Embryonic Divisions.
Cell · 2016 · 165(2): 396-409
Multiple division cycles without growth are a characteristic feature of early embryogenesis. The female germline loads proteins and RNAs into oocytes to support these divisions, which lack many quality control mechanisms operating in somatic cells undergoing growth. Here, we describe …
PMID 27020753 DOI ↗
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Coordinate Nodal and BMP inhibition directs Baf60c-dependent cardiomyocyte commitment.
Genes & development · 2013 · 27(21): 2332-44
A critical but molecularly uncharacterized step in heart formation and regeneration is the process that commits progenitor cells to differentiate into cardiomyocytes. Here, we show that the endoderm-derived dual Nodal/bone morphogenetic protein (BMP) antagonist Cerberus-1 (Cer1) in embryonic stem cell …
PMID 24186978 DOI ↗
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Multiple layers of molecular controls modulate self-renewal and neuronal lineage specification of embryonic stem cells.
Human molecular genetics · 2008 · 17(R1): R67-75
Elucidating the molecular changes that arise during neural differentiation and fate specification is crucial for building accurate in vitro models of neurodegenerative diseases using human embryonic stem cells (hESCs). Here we review the importance of hESCs and derived progenitors in …
PMID 18632700 DOI ↗
Datasets 25+
Multi-Modal Comparison of human Hepatic Stellate Cells identifies novel therapeutic targets for Metabolic Dysfunction-Associated Steatotic Liver Disease
Homo sapiens · GPL24676, GPL37309
Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved insulin secretion by pancreatic β cells
Mus musculus · GPL13112
An In Vivo Genome-Wide CRISPR Screen Identifies the RNA-Binding Protein Staufen2 as a Key Regulator of Myeloid Leukemia
Homo sapiens · GPL16791
Next Generation Sequencing: in vivo genome-wide CRISPR sgRNA screen in primary cancer-initiating and propagating bcCML stem cells
Mus musculus · GPL21103
Integrative Genomic Analysis Reveals Widespread Enhancer Regulation by p53 in Response to DNA Damage
Mus musculus · GPL9115
Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
Homo sapiens · GPL15520
The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation
Mus musculus · GPL17543
Genome-wide maps of chromatin state and chromatin accessibility in CD8 T cell subsets
Mus musculus · GPL17021
MYC ChIP-seq in human pancreatic ductal adenocarcinoma cells
Homo sapiens · GPL16791
Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect splicingÂ
Homo sapiens · GPL11154
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling (Zfp697 transduced primary mouse myotubes ChIP-Seq)
Mus musculus · GPL21626
Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes [bulk RNA-seq]
Mus musculus · GPL24247
Global Identification of the miR-130a targetome in human HSPC Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML [CUT&RUN]
Homo sapiens · GPL18573
Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes [ATAC-seq]
Mus musculus · GPL24247
Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development [RNA-Seq]
Homo sapiens · GPL11154
Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development [Affymetrix]
Homo sapiens · GPL6244
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [ChIP-Seq]
Homo sapiens · GPL11154
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription
Homo sapiens · GPL11154
Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes [Microglia RNA-seq]
Mus musculus · GPL24247
Open chromatin regions at the single cell level of CD8+ T cells from the spleens of LCMV-Armstrong or LCMV-Clone 13 infected mice
Mus musculus · GPL24247
The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RNA-seq2]
Homo sapiens · GPL11154
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [GRO-Seq]
Homo sapiens · GPL16791
Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development [Illumina]
Homo sapiens · GPL13534
Showing first 25 dataset results.
Analyses 10
GSE271650 · 5 steps · RNA-Seq · code_examples
Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes. (2024)
GSE271651 · 8 steps · RNA-Seq · code_examples
Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes. (2024)
GSE271652 · 5 steps · ATAC-seq · code_examples
Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes. (2024)
GSE213469 · 2 steps · ATAC-seq · code_examples
Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection. (2023)
GSE120023 · 5 steps · OTHER · code_examples
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. (2019)
GSE120104 · 5 steps · ChIP-Seq · code_examples
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. (2019)
GSE120105 · 5 steps · OTHER · code_examples
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. (2019)
GSE120110 · 5 steps · GSE · code_examples
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. (2019)
GSE68618 · 11 steps · ChIP-Seq · code_examples
Pseudotemporal Ordering of Single Cells Reveals Metabolic Control of Postnatal β Cell Proliferation. (2017)
GSE95237 · 3 steps · ChIP-Seq · code_examples
Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing. (2017)