John L. Rinn

Impaired synthesis of both telomere strands and adaptive TERT reduction in RTEL1 ATPase-dead cells

This study shows RTEL1 ATPase activity is essential for both telomere strand synthesis and TERT regulation, with reduced TERT providing an adaptive survival mechanism in RTEL1-defective cells.

Attenuated estrogen signaling disrupts placentation and drives trophoblast defects in Down syndrome

This study identifies attenuated estrogen signaling and NRIP1 as key factors in trophoblast defects in Down syndrome using patient-derived stem cells.

Temporal Transcriptomics Identifies Isoform-specific Trans-regulation by Multiple lncRNAs in Human iPSCs

The paper identifies six lncRNAs that regulate gene expression in trans in human iPSCs, revealing isoform-specific effects and a systemic response to doxycycline exposure.

Biophysical characterization of high-confidence, small human proteins

The paper characterizes biophysical properties of small human proteins, finding significant differences compared to larger proteins and providing insights for distinguishing functional from non-coding small open reading frames.

Massively Parallel Dissection of RNA in RNA-protein interactions in vivo

The paper introduces MPRNA-IP, a method to dissect RNA-protein interactions in vivo using custom RNA pools and statistical models to identify binding domains and structures.

Evaluation of the RNA-dependence of PRC2 binding to chromatin in human pluripotent stem cells

The paper evaluates the RNA-dependence of PRC2 chromatin binding in human pluripotent stem cells using optimized rChIP-seq and mutant analyses, supporting original findings.

Discovery and characterization of LNCSOX17 as an essential regulator in human endoderm formation

The paper identifies and characterizes LNCSOX17, a lncRNA essential for human endoderm formation, showing its role in regulating transcriptome and differentiation.

The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation

This study investigates the temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation, showing rapid and persistent effects on gene expression.

In vivo single-cell profiling of lncRNAs during Ebola virus infection

This study profiles lncRNA expression in single cells during Ebola virus infection in vivo, revealing cell-type specific changes and potential roles in immune response and viral hijacking.

Genome-wide binding analysis of 195 DNA Binding Proteins reveals "reservoir" promoters and human specific SVA-repeat family regulation

The paper re-analyzes ENCODE data to identify reservoir promoters and human-specific SVA-repeat regulation using reproducible methods.

Diverse mechanisms for epigenetic imprinting in mammals

This study investigates epigenetic mechanisms in mammals, revealing distinct roles of DNA methylation and Polycomb group repressors in autosomal imprinting and identifying unique pathways in the extraembryonic ectoderm.

Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency

The paper uses CRISPR interference to identify lncRNA loci critical for differentiation and pluripotency in human embryonic stem cells.

Myosin 7b is a regulatory long noncoding RNA (lncMYH7b) in the human heart

The paper identifies lncMYH7b as a regulatory long noncoding RNA in the human heart that influences the ratio of β-MyHC to α-MyHC through TEAD1/TEAD3 regulation, independent of miR-499.

Trans- and cis-acting effects of the lncRNA Firre on epigenetic and structural features of the inactive X chromosome

This study shows that Firre RNA has trans-acting effects on the inactive X chromosome, affecting histone modifications, PRC2 complex components, and chromatin structure.

Resolving mechanisms of immune-mediated disease in primary CD4 T cells

The paper identifies a causal variant in a super-enhancer that disrupts an NF-κB regulatory circuit, leading to T-cell activation in immune-mediated diseases.

Analysis of regulatory element evolution between human and mouse reveals a lack of cis-trans compensation

The paper measures cis and trans effects on regulatory elements between human and mouse to show cis-trans compensation is uncommon within individual elements.

In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation

This study shows that Firre and Dxz4 deletions in mice affect autosomal gene regulation without impacting XCI.

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue-specificity

The paper uses computational methods and MPRA to analyze lncRNA and mRNA promoters, finding that divergent promoters have higher transcriptional activity and lower tissue-specificity, while lincRNAs and eRNAs are more tissue-specific with simpler TF motif profiles.

The Tug1 Locus is Essential for Male Fertility

The paper identifies Tug1 as essential for male fertility, showing it has three distinct regulatory activities: a cis DNA repressor, a trans-acting lncRNA, and a conserved peptide affecting mitochondrial function.

Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of reprogramming outcome

The paper analyzes MYOD-mediated reprogramming of human fibroblasts using single-cell RNA-Seq to identify molecular determinants of reprogramming success and failure.

High-throughput identification of RNA nuclear enrichment sequences

The paper identifies RNA sequences responsible for nuclear enrichment in lncRNAs using a modified MPRA approach and validates findings with smRNA-FISH.

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

The paper identifies differences in chromatin environment, transcriptional regulation, and splicing between lincRNAs and mRNAs in human cell lines.

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

The paper uses pseudotemporal ordering to analyze single-cell data and reveals dynamics and regulators of cell fate decisions.