New paper in Cell

 2018 Dec 10. pii: S0092-8674(18)31518-6. doi: 10.1016/j.cell.2018.11.026. [Epub ahead of print]

Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity.

Abstract

Transcriptional regulation in metazoans occurs through long-range genomic contacts between enhancers and promoters, and most genes are transcribed in episodic “bursts” of RNA synthesis. To understand the relationship between these two phenomena and the dynamic regulation of genes in response to upstream signals, we describe the use of live-cell RNA imaging coupled with Hi-C measurements and dissect the endogenous regulation of the estrogen-responsive TFF1 gene. Although TFF1 is highly induced, we observe short active periods and variable inactive periods ranging from minutes to days. The heterogeneity in inactive times gives rise to the widely observed “noise” in human gene expression and explains the distribution of protein levels in human tissue. We derive a mathematical model of regulation that relates transcription, chromosome structure, and the cell’s ability to sense changes in estrogen and predicts that hypervariability is largely dynamic and does not reflect a stable biological state.

KEYWORDS:

RNA; chromosome; estrogen; fluorescence; heterogeneity; imaging; live-cell; single-molecule; steroid; transcription

PMID: 30554876

 

DOI: 10.1016/j.cell.2018.11.026
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New paper on GWAS

 2018 Dec;42(8):783-795. doi: 10.1002/gepi.22161. Epub 2018 Sep 24.

The accuracy of LD Score regression as an estimator of confounding and genetic correlations in genome-wide association studies.

Author information

1
Department of Psychology, University of Minnesota Twin Cities, Minneapolis, Minnesota.
2
Mathematical Biology Section, Laboratory of Biological Modeling, NIDDK, National Institutes of Health, Bethesda, Maryland.

Abstract

To infer that a single-nucleotide polymorphism (SNP) either affects a phenotype or is linkage disequilibrium with a causal site, we must have some assurance that any SNP-phenotype correlation is not the result of confounding with environmental variables that also affect the trait. In this study, we study the properties of linkage disequilibrium (LD) Score regression, a recently developed method for using summary statistics from genome-wide association studies to ensure that confounding does not inflate the number of false positives. We do not treat the effects of genetic variation as a random variable and thus are able to obtain results about the unbiasedness of this method. We demonstrate that LD Score regression can produce estimates of confounding at null SNPs that are unbiased or conservative under fairly general conditions. This robustness holds in the case of the parent genotype affecting the offspring phenotype through some environmental mechanism, despite the resulting correlation over SNPs between LD Scores and the degree of confounding. Additionally, we demonstrate that LD Score regression can produce reasonably robust estimates of the genetic correlation, even when its estimates of the genetic covariance and the two univariate heritabilities are substantially biased.

KEYWORDS:

causal inference; genetic correlation; heritability; population stratification; quantitative genetics

PMID:

 

30251275

 

DOI:

 

10.1002/gepi.22161

The low carb war continues

Last month, a paper in the British Journal of Medicine on the effect of low carb diets on energy expenditure, with senior author David Ludwig, made a big splash in the popular press and also instigated a mini-Twitter war. The study, which cost somewhere in the neighborhood of 12 million dollars, addressed the general question of whether a person will burn more energy on a low carbohydrate diet compared to an average or high carb diet. In particular, the study looked at the time period after weight loss where people are susceptible to regaining weight. The argument is that it will be easier to maintain weight loss on a low carb diet since you will be burning more energy. Recent intensive studies by my colleague Kevin Hall and others have found that low carb diets had little effect if any on energy expenditure, so this paper was somewhat of a surprise and gave hope to low carb aficionados. However, Kevin found some possible flaws, which he points out in an official response to BMJ and a BioRxiv paper, which then prompted a none-too-pleased response from Ludwig, which you can follow on Twitter. The bottom line is that the low carb effect size depends on the baseline point you compare too. In the original study plan, the baseline point was chosen to be energy expenditure prior to the weight loss phase of the study. In the publication, the baseline point was changed to after the weight loss but before the weight loss maintenance phase. If the original baseline was chosen, the low carb effect is no longer significant. The authors claim that they were blinded to the data and changed the baseline for technical reasons so this did not represent a case of p-hacking where one tries multiple combinations until something significant turns up. It seems pretty clear to me that low carbs do not have much of a metabolic effect but that is not to say that low carb diets are not effective. The elephant in the room is still appetite. It is possible that you are simply less hungry on a low carb diet and thus you eat less. Also, when you eliminate a whole category of food, there is just less food to eat. That could be the biggest effect of all.