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Article
Integrative analyses highlight functional regulatory variants associated with neuropsychiatric diseases
Noncoding variants of presumed regulatory function contribute to the heritability of neuropsychiatric disease. A total of 2,221 noncoding variants connected to risk for ten neuropsychiatric disorders, includin...
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Article
Advances in cutaneous squamous cell carcinoma
Human malignancies arise predominantly in tissues of epithelial origin, where the stepwise transformation from healthy epithelium to premalignant dysplasia to invasive neoplasia involves sequential dysregulati...
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Article
Open AccessSpatially resolved clonal copy number alterations in benign and malignant tissue
Defining the transition from benign to malignant tissue is fundamental to improving early diagnosis of cancer1. Here we use a systematic approach to study spatial genome integrity in situ and describe previously ...
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Article
PROBER identifies proteins associated with programmable sequence-specific DNA in living cells
DNA–protein interactions mediate physiologic gene regulation and may be altered by DNA variants linked to polygenic disease. To enhance the speed and signal-to-noise ratio (SNR) in the identification and quant...
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Article
Open AccessMutant collagen COL11A1 enhances cancerous invasion
Collagens are the most abundant proteins in the body and comprise the basement membranes and stroma through which cancerous invasion occurs; however, a pro-neoplastic function for mutant collagens is undefined...
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Article
The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation
Transcription factors bind DNA sequence motif vocabularies in cis-regulatory elements (CREs) to modulate chromatin state and gene expression during cell state transitions. A quantitative understanding of how moti...
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Article
Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but does not capture their spatial distribution nor reveal local networks of intercellular communication acting in situ. A su...
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Article
Open AccesseasyCLIP analysis of RNA-protein interactions incorporating absolute quantification
Quantitative criteria to identify proteins as RNA-binding proteins (RBPs) are presently lacking, as are criteria to define RBP target RNAs. Here, we develop an ultraviolet (UV) cross-linking immunoprecipitatio...
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Article
Open AccessStructural modularity of the XIST ribonucleoprotein complex
Long noncoding RNAs are thought to regulate gene expression by organizing protein complexes through unclear mechanisms. XIST controls the inactivation of an entire X chromosome in female placental mammals. Her...
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Article
Open AccessGenome-wide meta-analysis identifies eight new susceptibility loci for cutaneous squamous cell carcinoma
Cutaneous squamous cell carcinoma (SCC) is one of the most common cancers in the United States. Previous genome-wide association studies (GWAS) have identified 14 single nucleotide polymorphisms (SNPs) associa...
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Article
Open AccessKRAS regulation by small non-coding RNAs and SNARE proteins
KRAS receives and relays signals at the plasma membrane (PM) where it transmits extracellular growth factor signals to downstream effectors. SNORD50A/B were recently found to bind KRAS and inhibit its tumorige...
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Article
HiChIRP reveals RNA-associated chromosome conformation
Modular domains of long non-coding RNAs can serve as scaffolds to bring distant regions of the linear genome into spatial proximity. Here, we present HiChIRP, a method leveraging bio-orthogonal chemistry and o...
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Article
Author Correction: Methods to study RNA–protein interactions
In the version of this paper originally published, three references were accidentally omitted: Schwartz, J. C. et al. Cell Rep. 5, 918–925 (2013); Tundup, S. et al. FEBS Lett. 580, 1285–1293 (2006); and Itri, F. ...
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Article
Methods to study RNA–protein interactions
Noncoding RNA sequences, including long noncoding RNAs, small nucleolar RNAs, and untranslated mRNA regions, accomplish many of their diverse functions through direct interactions with RNA-binding proteins (RB...
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Article
Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment
Human embryonic stem cell (hESC) differentiation promises advances in regenerative medicine1–3, yet conversion of hESCs into transplantable cells or tissues remains poorly understood. Using our keratinocyte diffe...
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Correction: Corrigendum: RNA–protein interaction detection in living cells
Nat. Methods 15, 207–212 (2018); published online 5 February 2018; corrected after print 20 April 2018 In the version of this Article originally published, an amino acid substitution introduced into the B. sub...
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Article
Transcript-indexed ATAC-seq for precision immune profiling
T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide–major histocompatibility complex (MHC) ligands. He...
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Article
The functions and unique features of long intergenic non-coding RNA
Long intergenic non-coding RNAs (lincRNAs) are autonomously transcribed RNAs of more than 200 nucleotides in length that do not overlap protein-coding genes. T...
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Article
RNA–protein interaction detection in living cells
RaPID uses biotin ligases BirA* and the faster acting BASU to label proteins in the proximity of an RNA motif of interest in living cells.
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Article
Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements
High-resolution contact maps of active enhancers and target genes generated by H3K27ac HiChIP in primary human cells provide rational guides to link noncoding disease-associated risk variants to candidate caus...
