Patrick Cramer

The paper determines the cryo-EM structure of cytoplasmic Pol II and shows Gdown1 inhibits its transcriptional activity by blocking essential factor binding.

This study investigates the role of the +1 nucleosome in transcription initiation and the transition to elongation using in vitro experiments and cryo-EM structures.

This study reveals the molecular mechanisms of cap-snatching by influenza polymerase using cryo-EM structures of FluPol bound to Pol II and DSIF.

This study reveals a three-step mechanism of co-transcriptional H3K36 methylation by SETD2 through cryo-EM structures and functional analysis.

The paper introduces chemical crosslinking with mass spectrometry and a new search engine, NuXL, to identify nucleic acid-protein crosslinks at amino acid resolution, enhancing structural analysis.

The paper reports the cryo-EM structure of a transcribing Pol II-U1 snRNP complex with DSIF and SPT6, showing how phosphorylated Pol II and SPT6 interact with U1 snRNP to facilitate spliceosome assembly and transcription processivity.

This study identifies STK19 as a factor facilitating the transition from initial TCR complex assembly to downstream repair steps by enabling RNAPII clearance.

This study reveals how ELF2, a pioneer transcription factor, remodels nucleosomes near transcription start sites by unwrapping DNA and exposing chromatin, facilitating transcription initiation.

The paper identifies a three-step mechanism for RNA polymerase II promoter escape using in vitro reconstitution and structural analysis.

This study reconstitutes chromatin domains in vitro using S. cerevisiae and shows that nucleosome positioning alone is sufficient for domain formation.

This study determines the structural basis of RNA polymerase II initiation at snRNA promoters using SNAPc, revealing its role in DNA opening and transcription initiation independent of TFIIE and TFIIH.

This study shows Oct4 primarily activates transcription of pluripotency enhancers rather than controlling their chromatin accessibility.

The paper identifies sequence determinants of human gene regulatory elements by analyzing transcriptional activity of long DNA sequences in three cell types, revealing distinct enhancer types and TF subtypes based on motif content and activity patterns.

This study uses TT-seq to analyze RNA synthesis dynamics in three mouse pluripotent states, finding reduced RNA synthesis and elongation velocity in 2i and mTORi states.

The paper determines the structure of the human Mediator-RNA polymerase II transcription pre-initiation complex using cryo-EM, revealing interactions and conformational changes involved in transcription initiation.

The paper reports a dimeric structure of SARS-CoV-2 RdRp and suggests it may facilitate template switching during transcription.

The paper reports the cryo-EM structure of a mammalian transcribing RNA polymerase II-U1 snRNP complex and describes its role in co-transcriptional splicing.

The paper investigates mRNA buffering in yeast and finds that total mRNA concentration is buffered globally rather than gene-specifically.

The paper determines the in-cell architecture of a transcribing and translating expressome in Mycoplasma pneumoniae using integrative structural methods.

The paper reports the cryo-EM structure of CHD4 bound to a nucleosome, explaining how mutations in CHD4 contribute to cancer and intellectual disability.

The paper determines the structure of the yeast RSC chromatin remodeller bound to a nucleosome, revealing mechanisms of nucleosome sliding and implications for human SWI/SNF complexes and cancer.

NASC-seq monitors newly synthesized RNA in single cells, revealing dynamic gene expression during T-cell activation.

The paper determines the cryo-EM structure of the human core TFIIH-XPA-DNA complex, revealing how XPA and XPG switch TFIIH from a transcription factor to a DNA repair factor.

This paper presents a computational pipeline for analyzing TT-seq data to quantify RNA kinetic parameters and enhancer activity.

The paper introduces nano-ID, a method using nanopore sequencing and machine learning to study RNA isoform synthesis and stability, revealing differences in metabolism between individual isoforms and gene-level estimates.

The paper investigates how transcription factors interact with nucleosomal DNA, finding that most have less access to it than free DNA and that nucleosome structure affects motif positioning and orientation.

This study shows that RNA polymerase II CTDs undergo phase separation, forming clusters that are regulated by phosphorylation and CTD length.

Unspliced versus spliced mRNA in standard scRNA-seq gives RNA velocity, a per-cell vector predicting future state over hours, validated in neural crest and used to trace mouse hippocampal lineages.

GenoSTAN improves promoter and enhancer identification in 127 cell types and tissues, showing higher accuracy and better enrichment of genetic variants.

The paper defines sequence elements that regulate RNA metabolism in S. pombe by improving genome annotation and combining RNA labeling with mathematical modeling.