CiBER-seq dissects genetic networks
Cells integrate environmental signals and internal states to dynamically control gene expression. Muller et al. developed a technique to dissect this cellular logic by linking targeted, genome-wide genetic perturbations with a deep-sequencing readout that quantitatively measured the expression phenotype induced by each perturbation. The method, dubbed CiBER-seq, was able to recapitulate known regulatory pathways linking protein synthesis with nutrient availability in budding yeast cells. Unexpectedly, the authors found that the cellular logic also appears to consider protein production machinery in this decision. By uncovering additional facets of this deeply conserved pathway, the findings demonstrate the utility of comprehensive and quantitative CiBER-seq profiling in mapping the gene networks underlying cellular decisions.
Science, this issue p. eabb9662
Systematically profiling the effects of genetic perturbations is a powerful approach that has revealed the molecular basis for a wide range of biological phenomena. The simple, programmable DNA recognition of CRISPR-Cas9 enables genome-wide genetic analysis in human cells and many other systems. Cas9 is guided by a short RNA to a complementary sequence in the genome, where it can introduce mutations or alter gene expression. Pooled libraries of guide RNAs (gRNAs) that individually target each gene in the genome allow us to introduce genetic perturbations systematically into a population of cells. A key challenge is measuring the phenotypic effects caused by individual guides in these pooled libraries and linking these phenotypes back to the associated gRNA, thereby finding the gene that is responsible.
Molecular phenotypes such as gene expression changes provide a clear and sensitive measure for many cellular processes. We sought a general approach to profile how the expression of a particular gene of interest changed when other genes were perturbed. We began with a library of gRNAs, each disrupting one gene, and linked these guides with an expression reporter containing a guide-specific nucleotide barcode. gRNAs that alter reporter expression will change the abundance of the expressed RNA barcode specifically associated with that guide. Deep sequencing of these expressed barcodes quantifies each of these guide-specific reporter expression effects individually within a pooled, complex population. We have implemented this strategy by combining CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq).
We used CiBER-seq to profile the responses of several yeast promoters tied to a range of biological functions. Each promoter yielded a distinct pattern of responses that could be understood in terms of its known function and regulation. For example, we rediscover the control of MET6 expression by regulatory ubiquitylation and connect the bud scar protein Cwp1 to other genes required for budding and cytokinesis. Our analysis of the HIS4 promoter, a well-characterized target of the integrated stress response, yielded a range of genetic perturbations that activate this pathway by causing the accumulation of uncharged transfer RNAs (tRNAs). We also uncovered a notable role for tRNA depletion in this response, as impaired tRNA biogenesis activated HIS4 expression through a distinct pathway. In order to understand this regulation, we carried out genetic interaction analysis and looked for quantitative deviations in CiBER-seq profiles caused by the introduction of a second genetic perturbation. We also developed an indirect CiBER-seq approach to measure translational and posttranslational regulation, which both play roles in the signaling pathways upstream of HIS4.
CiBER-seq produces comprehensive phenotypic profiles that offer insights into gene function and regulation. These high-throughput and quantitative phenotypic measurements are also well suited for the systematic measurement of genetic interactions, which contain rich information about the operation of biological processes. This approach can be applied to study a wide range of transcriptional, translational, and posttranslational regulatory responses, and it has the potential to shed light on many areas of biology.
CRISPR-Cas9 gRNA cassettes are linked with transcriptional reporters containing specific barcodes. The RNA-to-DNA ratio for each barcode, measured by deep sequencing, reveals the reporter expression phenotype induced by each gRNA.
To realize the promise of CRISPR-Cas9based genetics, approaches are needed to quantify a specific, molecular phenotype across genome-wide libraries of genetic perturbations. We addressed this challenge by profiling transcriptional, translational, and posttranslational reporters using CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). Our barcoding approach allowed us to connect an entire library of guides to their individual phenotypic consequences using pooled sequencing. CiBER-seq profiling fully recapitulated the integrated stress response (ISR) pathway in yeast. Genetic perturbations causing uncharged transfer RNA (tRNA) accumulation activated ISR reporter transcription. Notably, tRNA insufficiency also activated the reporter, independent of the uncharged tRNA sensor. By uncovering alternate triggers for ISR activation, we illustrate how precise, comprehensive CiBER-seq profiling provides a powerful and broadly applicable tool for dissecting genetic networks.
- Age-related genetic changes in the blood associated with poor cancer prognosis - Medical Xpress - April 24th, 2025
- Parts of our DNA may evolve much faster than previously thought - The University of Utah - April 24th, 2025
- It runs in the family: the importance of genetics in pneumothorax - The BMJ - April 24th, 2025
- Inferring past demography and genetic adaptation in Spain using the GCAT cohort - Nature - April 24th, 2025
- Answers to a 160-year-old riddle about the genetics of Mendels pea traits - Nature - April 24th, 2025
- Towards a genetic obesity risk score in a single-center study of children and adolescents with obesity - Nature - April 24th, 2025
- Pan-genomic analysis highlights genes associated with agronomic traits and enhances genomics-assisted breeding in alfalfa - Nature - April 24th, 2025
- Study highlights critical diversity gap in psychiatric genomics research - Medical Xpress - April 24th, 2025
- Daily briefing: Potato pangenome reveals the complex genetics of the humble spud - Nature - April 24th, 2025
- Genetic diversity and adaptability of native sheep breeds from different climatic zones - Nature - April 24th, 2025
- Ginkgo Automation Partners with Aura Genetics to Accelerate Direct-to-Consumer Testing and Innovation - PR Newswire - April 24th, 2025
- Why Sarepta Therapeutics And Other Genetics Stocks Just Got A Sizable Boost - Investor's Business Daily - April 24th, 2025
- Why White Blood Cells were used to study genetic past and future of Indians - India Today - April 24th, 2025
- Association between plausible genetic factors and weight loss from GLP1-RA and bariatric surgery - Nature - April 24th, 2025
- Recent habitat modification of a tropical dry forest hotspot drives population genetic divergence in the Mexican leaf frog: a landscape genetics... - April 24th, 2025
- Barney's Farm Partners with Backpackboyz on Groundbreaking Cannabis Genetics Project - Ganjapreneur - Ganjapreneur - April 24th, 2025
- U.S. Preimplantation Genetic Testing Market Witness the Highest Growth Globally in Coming Years 2025-2034 - openPR.com - April 24th, 2025
- Exploring the implications of case selection methods for psychiatric molecular genetic studies - Nature - April 24th, 2025
- Genetic susceptibility to schizophrenia through neuroinflammatory pathways associated with retinal thinness - Nature - April 24th, 2025
- Who Were the Carthaginians? Ancient DNA Study Reveals a Stunning Answer - Haaretz - April 24th, 2025
- Genetics - National Geographic Society - March 28th, 2025
- Genetics: Introduction, law of inheritance and Sex Determination - BYJU'S - March 28th, 2025
- Genetics, ecology and evolution of phage satellites - Nature.com - March 28th, 2025
- As a geneticist, I will not mourn 23andMe and its jumble of useless health information | Adam Rutherford - The Guardian - March 28th, 2025
- Rare loss-of-function variants in HECTD2 and AKAP11 confer risk of bipolar disorder - Nature.com - March 28th, 2025
- With 23andMe filing for bankruptcy, what happens to consumers genetic data? - The Conversation Indonesia - March 28th, 2025
- A genetic tree as a movie: Moving beyond the still portrait of ancestry - Phys.org - March 28th, 2025
- Genetic mutations linked to Marek's disease in chickens identified - Phys.org - March 28th, 2025
- 23andMe is looking to sell customers genetic data. Heres how to delete it - CNN - March 28th, 2025
- Horses Pulled Off a Genetic Trick Only Viruses Were Thought to Use - SciTechDaily - March 28th, 2025
- CONSUMER ALERT: Warning 23AndMe Customers That Their Private Genetic Data May Be at Risk - Office of the Attorney General for the District of Columbia - March 28th, 2025
- A new study reveals the genetic change that made horses so athletic - KUOW News and Information - March 28th, 2025
- "Mystery ancestors" gave humans 20% of our current DNA, but who were they? - Earth.com - March 28th, 2025
- Correcting the Mutation Behind a Genetic Eye Disease - The Scientist - March 28th, 2025
- Your DNA is safe here: The AncestryDNA Genetic Test Kit is only $39 now - New York Post - March 28th, 2025
- 23andMe Is Bankrupt. Heres What You Need to Know About Your Genetic Data. - The Wall Street Journal - March 28th, 2025
- Commentary: 23andMe files for bankruptcy, putting its hoard of personal health information at risk - Los Angeles Times - March 28th, 2025
- DNA Microscopy Creates 3D Maps of Life From the Inside Out - SciTechDaily - March 28th, 2025
- Eugenics Must Be Included in Genetics Curriculum: Prof - Mirage News - March 28th, 2025
- 11-minute video on human genetics can make people more accepting of others, reveals new study - Hindustan Times - February 24th, 2025
- Advancing Cancer Genetic Testing to Improve Prevention and Patient Treatment - The Scientist - February 24th, 2025
- Environmental factors, lifestyle choices have greater impact on health than genes, study finds - ABC News - February 24th, 2025
- Study finds lifestyle, environment have greater impact on lifespan than genetics - CBS Boston - February 24th, 2025
- Safeguard repressor locks hepatocyte identity and blocks liver cancer - Nature.com - February 24th, 2025
- Mass spectrometry-based mapping of plasma protein QTLs in children and adolescents - Nature.com - February 24th, 2025
- The Avestagenome Project and TIGS Sign Strategic Alliance to Advance Research in Rare Genetic Disorders - The Tribune India - February 24th, 2025
- Researchers make breakthrough discovery after studying genetics of trees: 'There is a need for proactive conservation' - MSN - February 24th, 2025
- iPSCs and iPSC-derived cells as a model of human genetic and epigenetic variation - Nature.com - February 24th, 2025
- Beyond genetics: The biggest factors that influence health and aging - Earth.com - February 24th, 2025
- Genetic diversity and dietary adaptations of the Central Plains Han Chinese population in East Asia - Nature.com - February 24th, 2025
- How a uniquely human genetic tweak changed the voices of mice - NPR - February 24th, 2025
- Genetic evidence identifies a causal relationship between EBV infection and multiple myeloma risk - Nature.com - February 24th, 2025
- Genetic markers of early response to lurasidone in acute schizophrenia - Nature.com - February 24th, 2025
- Bupa to offer first genetic test for disease prediction in UK - The Times - February 24th, 2025
- Advancing Therapeutic Knowledge of Genetic Influence in ALS: Matthew B. Harms, MD - Neurology Live - February 24th, 2025
- Association of dietary carbohydrate ratio, caloric restriction, and genetic factors with breast cancer risk in a cohort study - Nature.com - February 24th, 2025
- Evaluation of polygenic scores for hypertrophic cardiomyopathy in the general population and across clinical settings - Nature.com - February 24th, 2025
- Familiar autism-linked genes emerge from first analysis of Latin American cohort - The Transmitter: Neuroscience News and Perspectives - February 24th, 2025
- Almost 90% of people would agree to genetic testing to tailor medication use, survey finds - Medical Xpress - February 24th, 2025
- Largest Genetic Study of Bipolar Disorder Identifies 298 Regions of the Genome That Increase Risk for the Condition - Mount Sinai - January 27th, 2025
- Study Sheds Light On The Origin Of Earth Lifes Genetic Code - Astrobiology News - January 27th, 2025
- Largest study on the genetics of bipolar disorder to date gives new insights into the underlying biology - Medical Xpress - January 27th, 2025
- Genetic Swiss Army Knife: New Tool For Gene Editing And Therapy - Forbes - January 27th, 2025
- Uhm Ji-won says the power of genetics is undeniable with Hyun Bin and Son Ye-jin's son - - January 27th, 2025
- Integrative proteogenomic analysis identifies COL6A3-derived endotrophin as a mediator of the effect of obesity on coronary artery disease -... - January 27th, 2025
- Genetic analysis reveals the genetic diversity and zoonotic potential of Streptococcus dysgalactiae isolates from sheep - Nature.com - January 27th, 2025
- Eight psychiatric disorders share the same genetic causes, study says - Medical Xpress - January 27th, 2025
- Exploring genetic associations and drug targets for mitochondrial proteins and schizophrenia risk - Nature.com - January 27th, 2025
- Predictive Genetic Testing and Consumer Genomics Market - GlobeNewswire - January 27th, 2025
- Evolution without sex: How mites have survived for millions of years - EurekAlert - January 27th, 2025
- Our Understanding of Rules that Produce Lifes Genetic Code May Require a Revision - DISCOVER Magazine - January 27th, 2025
- Personalized therapy for rare genetic diseases: Patient-derived organoids offer new hope - Medical Xpress - January 27th, 2025
- The One Thing That's More Important for Longevity Than Your Genes - Parade Magazine - January 27th, 2025
- Complete recombination map of the human genome created - Medical Xpress - January 27th, 2025
- Evidence of genetic determination of annual movement strategies in medium-sized raptors - Nature.com - January 27th, 2025
- Genetic study of Alaska red king crabs suggests species is more diverse and resilient to climate change - Global Seafood Alliance - January 27th, 2025
- Smartwatches reveal insights into psychiatric illnesses and genetic links - Medical Xpress - January 27th, 2025
- Unlocking the Blueprint of Human Life With a Revolutionary DNA Map - SciTechDaily - January 27th, 2025
- Largest Genetic Study of Bipolar Disorder Identifies Nearly 300 Risk-Associated Genome Regions - Inside Precision Medicine - January 27th, 2025
- Genetic Discrimination Is Coming for Us All - The Atlantic - November 16th, 2024