Stirling Churchman (@fiddle) / X

Stirling Churchman

1,444 posts

Stirling Churchman

@fiddle

@HMSgenetics professor studying RNA dynamics across the cell, including transcription, mRNA processing, and mitochondrial gene expression. @Stanford physics PhD

Cambridge, MA

churchman.med.harvard.edu

Joined November 2007

Pinned
Stirling Churchman
@fiddle
Mar 22, 2024
I'm thrilled to see the cover of @NatureSMB this month! My sibling Leidy Churchman made this special painting to illustrate our latest work on the packaging of mitochondrial DNA. Both works are nicely described in the "Musings on art and science" editorial nature.com/articles/s4159…
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Stirling Churchman
@fiddle
Apr 12, 2020
What did you guys do yesterday? I got married on zoom! @AndyStrominger
Stirling Churchman
@fiddle
Nov 22, 2017
It’s official, the best lab website is the Heiman lab website! It’s a must see, but make sure you have some time to kill. heimanlab.com/cgi-bin/heiman
Stirling Churchman
@fiddle
Aug 22, 2022
How does RNA flow through the cell? From their synthesis, chromatin release, nuclear export, ribosome engagement, and eventual degradation, we quantified the lives of human transcripts genome-wide. (1/7) See @BrendanSmalec and @robertietswaart ‘s preprint
biorxiv.org
Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the...
Dissecting the myriad regulatory mechanisms controlling eukaryotic transcripts from production to degradation requires quantitative measurements of mRNA flow across the cell. We developed subcellular...
Stirling Churchman
@fiddle
Aug 15, 2022
Splicing of human introns could occur in any order across an RNA, which combinatorially adds up to thousands of possible splicing orders for a typical transcript. Are all orders used? Read our latest preprint by @Karine_Choquet to find out! (1/6)
biorxiv.org
Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic...
Combinatorially, intron excision within a given nascent transcript could proceed down any of thousands of paths, each of which would expose different dynamic landscapes of cis-elements and contribute...
Stirling Churchman
@fiddle
Sep 5, 2019
Ever had a list of gene hits and not known what to do? Maybe GO enrichment left you wondering what your favorite gene is doing in your experiment? Check out GeneWalk, our #ML method that determines the relevant functions for each gene @robertietswaart (1/4)
biorxiv.org
GeneWalk identifies relevant gene functions for a biological context using network representation...
The primary bottleneck in high-throughput genomics experiments is identifying the most important genes and their relevant functions from a list of gene hits. Existing methods such as Gene Ontology...
Stirling Churchman
@fiddle
Feb 2, 2021
GeneWalk is now published! Ever had a list of gene hits and not known what to do? Maybe GO enrichment left you wondering what your favorite gene is doing in your experiment? GeneWalk determines the relevant functions for every gene hit! @robertietswaart
Genome Biology
@GenomeBiology
Feb 2, 2021
GeneWalk, from @robertietswaart, @fiddle and co, is a method for prioritizing genes from a gene list. Given a list of genes, eg from RNA-seq experiment, it constructs a regulatory network and uses GO annotations to identify the most relevant genes. genomebiology.biomedcentral.com/articles/10.11…
Stirling Churchman
@fiddle
Sep 26, 2022
How are the hundreds of copies of mitochondrial DNA packaged in our cells? It’s a mystery because histones and chromatin factors are not in mitochondria and the high copy number presents challenges! Read what Stefan @RsIsaac found in our preprint. (1/7)
biorxiv.org
Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA
Cellular metabolism relies on the regulation and maintenance of mitochondrial DNA (mtDNA). Hundreds to thousands of copies of mtDNA exist in each cell, yet because mitochondria lack histones or other...
Stirling Churchman
@fiddle
Jan 29, 2021
Our protocol for direct sequencing of nascent RNA is now published! Nanopore analysis of CO-transcriptional Processing (nano-COP) took us four years to get right. In this protocol, we describe the final approach *and* how we got there. (1/3) rdcu.be/cergf
Stirling Churchman
@fiddle
Apr 16, 2019
Human genes have so many introns! When and how are they all spliced out? Does splicing follow the order of transcription? Are neighboring introns spliced cooperatively? These fundamental questions are crucial to our understanding of splicing regulation. (1/4)
Stirling Churchman
@fiddle
Jun 1, 2021
Human respiratory complexes are encoded on both nuclear and mitochondrial DNA. Is gene expression coordinated across these genomes that are expressed in separate compartments and by different factors? Read our latest preprint to find out! (1/7)
biorxiv.org
Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory...
Oxidative phosphorylation (OXPHOS) complexes consist of nuclear and mitochondrial DNA-encoded subunits. Their biogenesis requires cross-compartment gene regulation to mitigate the accumulation of...
Stirling Churchman
@fiddle
Jan 3, 2024
How does Pol II navigate the crowded, complex chromatin environment, surrounded by nucleosomes and other transcriptional activity? We are excited to share our preprint, a fantastic collaboration with @stergachislab, led by Tommy Tullius @mtcicero26 biorxiv.org/content/10.110… (1/5)
biorxiv.org
RNA polymerases reshape chromatin and coordinate transcription on individual fibers
During eukaryotic transcription, RNA polymerases must initiate and pause within a crowded, complex environment, surrounded by nucleosomes and other transcriptional activity. This environment creates...
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Stirling Churchman
@fiddle
Aug 5, 2024
churchman lab IS labrat
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Stirling Churchman
@fiddle
Feb 13, 2023
How are nuclear and mitochondrial DNA co-regulated to achieve balanced oxidative phosphorylation (OXPHOS) subunits? We performed a CRISPR screen to identify human genes that maintain mitonuclear balance. See our preprint by Nick Kramer and @GyPrak (1/4)
biorxiv.org
Genome-wide screens for mitonuclear co-regulators uncover links between compartmentalized metabol...
Mitochondrial oxidative phosphorylation (OXPHOS) complexes are assembled from proteins encoded by both nuclear and mitochondrial DNA. These dual-origin enzymes pose a complex gene regulatory challe...
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