The Post-Apoptotic Fate of RNAs Identified Through High-Throughput Sequencing of Human Hair

Stem Cell Program, Division of Dermatology, Department of Medicine, Institute for Genomic Medicine, University of California San Diego, San Diego, California, United States of America.
PLoS ONE (Impact Factor: 3.23). 11/2011; 6(11):e27603. DOI: 10.1371/journal.pone.0027603
Source: PubMed


The hair of all mammals consists of terminally differentiated cells that undergo a specialized form of apoptosis called cornification. While DNA is destroyed during cornification, the extent to which RNA is lost is unknown. Here we find that multiple types of RNA are incompletely degraded after hair shaft formation in both mouse and human. Notably, mRNAs and short regulatory microRNAs (miRNAs) are stable in the hair as far as 10 cm from the scalp. To better characterize the post-apoptotic RNAs that escape degradation in the hair, we performed sequencing (RNA-seq) on RNA isolated from hair shafts pooled from several individuals. This hair shaft RNA library, which encompasses different hair types, genders, and populations, revealed 7,193 mRNAs, 449 miRNAs and thousands of unannotated transcripts that remain in the post-apoptotic hair. A comparison of the hair shaft RNA library to that of viable keratinocytes revealed surprisingly similar patterns of gene coverage and indicates that degradation of RNA is highly inefficient during apoptosis of hair lineages. The generation of a hair shaft RNA library could be used as months of accumulated transcriptional history useful for retrospective detection of disease, drug response and environmental exposure.

Download full-text


Available from: Anandaroop Mukhopadhyay, Sep 08, 2014
  • [Show abstract] [Hide abstract]
    ABSTRACT: High throughput molecular biology began around the mid-1990s with the introduction of microarrays - a technology that enabled investigators to quantify the cellular expression levels of tens of thousands of mRNA transcripts simultaneously. To date, a large number of microarray experiments have been performed in the investigation of RNA expression signatures in normal and pathological tissues. This review focuses on a next generation tool in high throughput investigation: RNA sequencing or RNA-Seq, highlighting its advantages over traditional microarray investigation and discussing its utility in investigative dermatology. In contrast with the results obtained from microarray experiments, RNA-Seq generates mRNA abundance counts, can identify novel transcripts and splice variants, and provides sequence resolution at the level of single base-pairs. Implementing RNA-Seq in the investigation of skin disease will yield novel insights into the pathogenesis of disease, will facilitate the discovery of new diseases and new mechanisms of disease, and will allow researchers to probe genetic disease in high resolution and with unprecedented efficiency.
    No preview · Article · Apr 2012 · Australasian Journal of Dermatology
  • [Show abstract] [Hide abstract]
    ABSTRACT: Serum microRNA levels are known as useful biomarkers for various diseases. Recent publication has indicated the existence of microRNAs in hair roots and hair shafts. In this study, we evaluated several methods for the extraction of hair microRNAs, and their usefulness for the diagnosis of scleroderma. A single hair root and 5 pieces of hair shafts were obtained from the occiput of each individual of 11 scleroderma patients and 13 normal subjects at the time of serum sampling. microRNA extraction from sera or hair roots was performed with commercially available kits. microRNAs were extracted from hair shafts using four different methods. microRNA expression was evaluated by PCR array and real-time PCR. We demonstrated microRNAs in hair roots and hair shafts were detectable and quantitative using our method. We found the difference of microRNA levels in hair roots and hair shafts obtained from different places of head in each individual were within 2-fold, indicating the reproducibility of hair microRNA levels by our method. PCR array revealed microRNAs from sera, hair roots and hair shafts have different expression pattern, and can be independent biomarkers. Serum and hair root miR-196a levels were not significantly changed in scleroderma patients, while we found miR-196a levels in hair shafts were significantly decreased in scleroderma patients compared to those in normal subjects (p<0.05). Hairs are more accessible than sera among human samples. microRNAs levels in hair roots or hair shafts may become effective and independent biomarkers.
    No preview · Article · Jul 2013 · Journal of dermatological science
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: In the present study, we evaluated the possibility that we can utilize hair shaft miR-29a levels as disease marker of scleroderma. Hair samples were obtained from 20 scleroderma patients, 5 dermatomyositis patients and 13 controls. microRNAs were purified from hairs as well as skins or sera, and miR-29a levels were measured with quantitative real-time polymerase chain reaction Mean hair miR-29a levels in scleroderma patients were significantly lower than those in control subjects or dermatomyositis, while expression levels of hair shaft marker keratin 34 were similar among them. There was no strong correlation among the miR-29a levels in the hair, skin and serum of each patient, suggesting that hair microRNAs can be independent biomarkers. We found scleroderma patients with decreased miR-29a levels had contracture of the phalanges at a significantly higher prevalence than those without. To confirm the clinical usefulness of hair microRNAs, large-scale researches are needed in the future. This article is protected by copyright. All rights reserved.
    Full-text · Article · Sep 2013 · Experimental Dermatology
Show more