About

Iain M. Cheeseman is the Herman and Margaret Sokol Professor of Biology at MIT and a Core Member of the Whitehead Institute. His research focuses on analyzing the process by which cells duplicate, with particular emphasis on how the molecular machinery that segregates chromosomes is rewired across diverse physiological contexts. His work has concentrated on proteins that direct chromosome segregation and cell division, including the macromolecular kinetochore structure that mediates chromosome-microtubule interactions. Cheeseman investigates how core cellular structures like the kinetochore are modulated and rewired to adapt to different situations, exploring transcriptional, translational, and post-translational mechanisms that generate proteomic variability within individual cells and across tissues, cell states, development, and disease.

Research topics

• Biophysics
• Genetics
• Chemistry
• Cell biology
• Biology

Selected publications

• 5′ UTR length regulates alternative N-terminal protein isoform production in health and disease

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-22

  articleOpen accessSenior authorCorresponding

  Abstract The 5′ untranslated region (5′ UTR) of an mRNA is classically viewed as a regulatory region that controls the amount of protein production, but not the resulting protein sequence. Here, we demonstrate that 5′ UTR length plays a direct role in alternative N-terminal protein isoform production by controlling start codon selection. We find that very short 5′ UTRs enhance leaky ribosome scanning, thereby promoting the production of truncated alternative N-terminal protein isoforms. We also show that endogenous changes in 5′ UTR length due to alternative transcription initiation can tune the relative abundance of alternative N-terminal isoforms from the same gene. In addition, we identify mutations in rare genetic diseases that alter 5′ UTR length, including a deletion in the VHL 5′ UTR in von Hippel–Lindau disease that shifts translation toward the shorter VHLp19 isoform. Together, our results implicate 5′ UTR length as a determinant of alternative N-terminal isoform production and reveal an underappreciated mechanism by which noncoding changes can reshape the proteome. Highlights 5′ UTR length affects the landscape of endogenous alternative N-terminal protein isoforms Generation of an alternative truncated AKR7A2 isoform is mediated by short 5′ UTR length Alternative transcription initiation modulates 5′ UTR length to tune N-terminal isoform ratios Pathogenic VHL 5′ UTR variants perturb N-terminal isoform ratios by altering 5′ UTR length

  PublisherDOI

• 5′ UTR length shapes alternative N-terminal protein isoforms across cancers and in rare disease

  EMBO Reports · 2026-04-13

  articleOpen accessSenior authorCorresponding

  The 5' untranslated region (5' UTR) of an mRNA is classically viewed as a regulatory region that controls the amount of protein production, but not the resulting protein sequence. Here, we demonstrate that 5' UTR length plays a direct role in alternative N-terminal protein isoform production by controlling start codon selection. We find that very short 5' UTRs enhance leaky ribosome scanning, thereby promoting the production of truncated alternative N-terminal protein isoforms. We also show that endogenous changes in 5' UTR length due to alternative transcription initiation can tune the relative abundance of alternative N-terminal isoforms from the same gene. In addition, we identify mutations in rare genetic diseases that alter 5' UTR length, including a deletion in the VHL 5' UTR in von Hippel-Lindau disease that shifts translation toward the shorter VHLp19 isoform. Together, our results implicate 5' UTR length as a determinant of alternative N-terminal isoform production and reveal an underappreciated mechanism by which noncoding changes can reshape the proteome.

  PublisherOA PDFDOI

• P614: The importance of alternative transcript analysis in rare disease diagnosis: A case series

  Genetics in Medicine Open · 2026-01-01

  articleOpen access

  cholesterol measurements recorded in the EHR.Of 20 individuals evaluated for ASCVD, ten (50%) demonstrated evidence of disease, including coronary artery calcification, aortic valve sclerosis, carotid artery plaque or thickening, or infarct. Conclusion:This study expands the limited literature by demonstrating that multiple different heterozygous LP/P LDLRAP1 variants, in the absence of pathogenic variants in other hypercholesterolemia genes, co-occur with elevated LDL-C, hypercholesterolemic pharmacotherapy, signs of ASCVD, and a positive family history of elevated LDL-C and/or ASCVD.These results are supportive of a role for LDLRAP1 haploinsufficiency in hyperbetalipoproteinemia and imply that heterozygous individuals should be prompted to have their cholesterol measured and managed accordingly.Furthermore, consideration should be given to include LDLRAP1 in Tier 1 genetic screening for hypercholesterolemia.

  PublisherOA PDFDOI

• Regulation of mRNA decay and translation during the mammalian cell cycle

  RNA · 2026-02-05

  articleOpen accessSenior author

  Cell cycle progression requires cells to continually remodel their gene expression programs as they transition through distinct functional states. Although transcriptional and post-translational mechanisms have long dominated our understanding of this regulation, recent work additionally highlights the essential contribution of cell cycle–specific mRNA decay and translational control. Across G 1 , S, G 2 , and mitosis, cells dynamically modulate global and transcript-specific mRNA stability and translation to coordinate processes including DNA replication, growth, checkpoint signaling, and chromosome segregation. Mitosis presents a particularly striking challenge: Transcription is reduced, necessitating that cells rely on post-transcriptional mechanisms to sustain mitotic functions and preserve viability. In this review, we highlight how these coordinated layers of post-transcriptional regulation collectively contribute to cell cycle control.

  PublisherOA PDFDOI

• Global stabilization of the transcriptome in mitotic cells

  The EMBO Journal · 2026-04-09 · 1 citations

  articleOpen accessSenior author

  In the presence of cell division errors, mammalian cells can pause in mitosis for tens of hours with little to no transcription, while still requiring continued translation for viability. These unique aspects of mitosis require substantial adaptations to gene expression. During interphase, homeostatic control of mRNA levels involves a constant balance of transcription and degradation, with a median mRNA half-life of ~2-4 h. If such short half-lives persisted in mitosis, cells would be expected to rapidly deplete their transcriptome without new transcription. Here, we report that the transcriptome is globally stabilized during prolonged mitotic delays. Median mRNA half-lives are increased >4-fold during mitotic arrest compared to interphase, buffering mRNA levels in the absence of new synthesis. Moreover, poly(A) tail-length profiles change during mitotic arrest, strongly suggesting a partial mitotic repression of deadenylation. In contrast, siRNA-directed mRNA degradation machinery remains active. We further show that mitotic mRNA stabilization depends on PABPC1&4. Depletion of PABPC1&4 during mitotic arrest reduces mRNA stability and disrupts the cells' ability to maintain arrest, highlighting the critical physiological role of mitotic transcriptome buffering.

  PublisherOA PDFDOI

• The one-week automated genome-wide optical pooled screen

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-19

  articleOpen access

  Abstract Optical pooled screens (OPS) are bottlenecked by labor-intensive in situ sequencing and analysis protocols. Here we present OttoSeq, an automated OPS platform combining the Otto2 fluid handling system with the Brieflow analysis pipeline. We utilized OttoSeq to complete a genome-wide cell painting screen in eight days, sampling more than 5 million high-quality cells across 21,732 gene knockout perturbations (224 cells per gene) and interpreting 320 functional gene clusters.

  PublisherOA PDFDOI

• Differential roles for the spindle assembly checkpoint in error surveillance and mitotic timing

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-15

  preprintOpen accessSenior authorCorresponding

  Abstract The Spindle Assembly Checkpoint (SAC) plays critical roles in regulating mitotic fidelity and progression. Here, we utilized a SAC-deficient cell line lacking the full-length Cdc20 translational protein isoform (Cdc20 ΔFL) to define its differential genetic interactions using CRISPR/Cas9-based gene targeting. Cdc20 ΔFL cells display synthetic lethal relationships with gene targets required for proper chromosome segregation, highlighting the critical role of the SAC in error surveillance. Surprisingly, we found that the checkpoint component Mad2 becomes dispensable for viability in Cdc20 ΔFL cells. Prior work suggested that Mad2 acts as an essential mitotic “timer” to control mitotic duration in unperturbed cells. Instead, our functional analysis indicates that the mitotic timer depends on the interdependent and overlapping actions of: (1) Mad2 inhibition of APC/C-Cdc20, (2) Cdk1-mediated phosphorylation of Cdc20, and (3) total Cdc20 protein levels. Simultaneously perturbing these pathways results in near immediate mitotic exit and catastrophic chromosome mis-segregation.

  PublisherDOI

• Brieflow: An Integrated Computational Pipeline for High-Throughput Analysis of Optical Pooled Screening Data

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-27 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Optical pooled screening (OPS) has emerged as a powerful technique for functional genomics, enabling researchers to link genetic perturbations with complex cellular morphological phenotypes at unprecedented scale. However, OPS data analysis presents challenges due to massive datasets, complex multi-modal integration requirements, and the absence of standardized frameworks. Here, we present Brieflow, a computational pipeline for end-to-end analysis of fixed-cell optical pooled screening data. We demonstrate Brieflow's capabilities through reanalysis of a CRISPR-Cas9 screen encompassing 5,072 fitness-conferring genes, processing more than 70 million cells with multiple phenotypic markers. Our analysis reveals functional gene relationships that were missed in the original study, uncovering coherent biological insights related to mitochondrial function, mRNA processing, vesicular trafficking, and MYC transcriptional control, amongst others. The modular design and open-source implementation of Brieflow facilitates the integration of novel analytical components while ensuring computational reproducibility and improved performance for the use of high-content phenotypic screening in biological discovery.

  PublisherOA PDFDOI

• Alternative start codon selection shapes mitochondrial function during evolution, homeostasis, and disease

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-27

  preprintOpen accessSenior authorCorresponding

  Mitochondrial endosymbiosis was a pivotal event in eukaryotic evolution, requiring core proteins to adapt to function both within the mitochondria and in the host cell. Here, we systematically profile the localization of protein isoforms generated by alternate start codon selection during translation. We identify hundreds of pairs of differentially-localized protein isoforms, many of which affect mitochondrial targeting and are essential for mitochondrial function. The emergence of dual-localized mitochondrial protein isoforms coincides with mitochondrial acquisition during early eukaryotic evolution. We further reveal that eukaryotes use diverse mechanisms-such as leaky ribosome scanning, alternative transcription, and paralog duplication-to maintain the production of dual-localized isoforms. Finally, we identify multiple isoforms that are specifically dysregulated by rare disease patient mutations and demonstrate how these mutations can help explain unique clinical presentations. Together, our findings illuminate the evolutionary and pathological relevance of alternative translation initiation, offering new insights into the molecular underpinnings of mitochondrial biology.

  PublisherOA PDFDOI

• Molecular determinants of RNase MRP specificity and function

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-28 · 2 citations

  preprintOpen accessSenior authorCorresponding

  RNase MRP and RNase P are evolutionarily related complexes that facilitate rRNA and tRNA biogenesis, respectively. The two enzymes share nearly all protein subunits and have evolutionarily related catalytic RNAs. Notably, RNase P includes a unique subunit, Rpp21, whereas no RNase MRP-specific proteins have been found in humans, limiting molecular analyses of RNase MRP function. Here, we identify the RNase MRP-specific protein, C18orf21/RMRPP1. RMRPP1 and Rpp21 display significant structural homology, but we identify specific regions that drive interactions with their respective complexes. Additionally, we reveal that RNase MRP is required for 40S, but not 60S, ribosome biogenesis uncovering an alternative pathway for ribosome assembly. Finally, we identify Nepro as an essential rRNA processing factor that associates with the RNase MRP complex. Together, our findings elucidate the molecular determinants of RNase MRP function and underscore its critical role in ribosome biogenesis.

  PublisherDOI

Recent grants

• NIH Grant R01GM088313

  NIH · $3.6M · 2018

• Harnessing evolution to reveal the molecular logic of kinetochore wiring

  NSF · $1.2M · 2020–2024

• Molecular Analysis of Kinetochore Function

  NIH · $7.0M · 2018–2028

• NIH Grant R01GM108718

  NIH · $1.1M · 2019

• INNER CENTROMERE TARGETING OF THE CHROMOSOME PASSENGER COMPLEX

  NIH · $10.6M · 2011–2016

Frequent coauthors

• Arshad Desai

  Ludwig Cancer Research

  39 shared

• Tatsuo Fukagawa

  Osaka University

  38 shared

• Julie P. I. Welburn

  Wellcome Centre for Cell Biology

  32 shared

• Kuan-Chung Su

  Whitehead Institute for Biomedical Research

  31 shared

• Kara L. McKinley

  Howard Hughes Medical Institute

  28 shared

• Chelsea B. Backer

  Phillips Exeter Academy

  27 shared

• Julie K. Monda

  University of California, San Diego

  25 shared

• Nolan K. Maier

  Whitehead Institute for Biomedical Research

  23 shared

Labs

• Iain M. Cheeseman LabPI

Awards & honors

• Global Consortium for Reproductive Longevity and Equality (G…
• MIT Undergraduate Research Opportunities Program (UROP) Outs…
• American Society for Cell Biology (ASCB) Early Career Life S…
• Searle Scholar Award (2009-2012)