Nicolas J. Lehrbach

Bio: Nicolas J. Lehrbach is an academic researcher from Harvard University. The author has contributed to research in topics: Caenorhabditis elegans & Argonaute. The author has an hindex of 17, co-authored 28 publications receiving 2440 citations. Previous affiliations of Nicolas J. Lehrbach include University of Sydney & University of Cambridge.

Function, Targets, and Evolution of Caenorhabditis elegans piRNAs

Abstract: Piwi-interacting RNAs (piRNAs) are small RNAs required to maintain germline integrity and fertility, but their mechanism of action is poorly understood. Here we demonstrate that Caenorhabditis elegans piRNAs silence transcripts in trans through imperfectly complementary sites. Target silencing is independent of Piwi endonuclease activity or "slicing." Instead, piRNAs initiate a localized secondary endogenous small interfering RNA (endo-siRNA) response. Endogenous protein-coding gene and transposon transcripts exhibit Piwi-dependent endo-siRNAs at sites complementary to piRNAs and are derepressed in Piwi mutants. Genomic loci of piRNA biogenesis are depleted of protein-coding genes and tend to overlap the start and end of transposons in sense and antisense, respectively. Our data suggest that nematode piRNA clusters are evolving to generate piRNAs against active mobile elements. Thus, piRNAs provide heritable, sequence-specific triggers for RNA interference in C. elegans.

LIN-28 and the poly(U) polymerase PUP-2 regulate let-7 microRNA processing in Caenorhabditis elegans.

Abstract: Developmental expression of the microRNA let-7 is tightly regulated in many animals, and turnover has been linked to LIN-28 and uridylation in mammals. This regulation is now shown to be conserved in Caenorhabditis elegans, and PUP-2 is shown to be a uridylase that is specifically recruited to let-7 in a LIN-28–dependent manner. The let-7 microRNA (miRNA) is an ultraconserved regulator of stem cell differentiation and developmental timing and a candidate tumor suppressor. Here we show that LIN-28 and the poly(U) polymerase PUP-2 regulate let-7 processing in Caenorhabditis elegans. We demonstrate that lin-28 is necessary and sufficient to block let-7 activity in vivo; LIN-28 directly binds let-7 pre-miRNA to prevent Dicer processing. Moreover, we have identified a poly(U) polymerase, PUP-2, which regulates the stability of LIN-28–blockaded let-7 pre-miRNA and contributes to LIN-28–dependent regulation of let-7 during development. We show that PUP-2 and LIN-28 interact directly, and that LIN-28 stimulates uridylation of let-7 pre-miRNA by PUP-2 in vitro. Our results demonstrate that LIN-28 and let-7 form an ancient regulatory switch, conserved from nematodes to humans, and provide insight into the mechanism of LIN-28 action in vivo. Uridylation by a PUP-2 ortholog might regulate let-7 and additional miRNAs in other species. Given the roles of Lin28 and let-7 in stem cell and cancer biology, we propose that such poly(U) polymerases are potential therapeutic targets.

Proteasome dysfunction triggers activation of SKN-1A/Nrf1 by the aspartic protease DDI-1

Abstract: Proteins perform many important roles in cells, but these molecules can become toxic if they are damaged or are no longer needed. A molecular machine called the proteasome destroys ‘unwanted’ proteins in animal and other eukaryotic cells. If the proteasome stops working properly, unwanted proteins start to accumulate and cells respond by increasing the activity of genes that make proteasomes. A protein called SKN-1 is involved in this response and activates the genes that encode proteasome proteins, but it is not understood how SKN-1 “senses” that proteasomes are not working properly. Here, Lehrbach and Ruvkun used a roundworm called Caenorhabditis elegans to search for new genes that activate SKN-1 when the proteasome’s activity is impaired. The roundworms were genetically engineered to produce a fluorescent protein that indicates when a particular gene needed to make proteasomes is active. Lehrbach and Ruvkun identified some roundworms with mutations that cause the levels of fluorescence to be lower, indicating that SKN-1 was less active in these animals. Further experiments showed that some of these mutations are in genes that encode enzymes called DDI-1 and PNG-1. DDI-1 is able to cut certain proteins, while PNG-1 can remove sugars that are attached to proteins. Therefore, it is likely that these enzymes directly interact with SKN-1 and alter it to activate the genes that produce the proteasome. More work is now needed to understand the details of how modifying SKN-1 changes its activity in cells. In the future, drugs that target DDI-1 or PNG-1 might be used to treat diseases in which proteasome activity is too high or low, including certain cancers and neurodegenerative diseases.

The widespread regulation of microRNA biogenesis, function and decay.

Abstract: MicroRNAs (miRNAs) are a large family of post-transcriptional regulators of gene expression that are ~21 nucleotides in length and control many developmental and cellular processes in eukaryotic organisms. Research during the past decade has identified major factors participating in miRNA biogenesis and has established basic principles of miRNA function. More recently, it has become apparent that miRNA regulators themselves are subject to sophisticated control. Many reports over the past few years have reported the regulation of miRNA metabolism and function by a range of mechanisms involving numerous protein-protein and protein-RNA interactions. Such regulation has an important role in the context-specific functions of miRNAs.

Environmental epigenomics and disease susceptibility.

Abstract: Epidemiological evidence increasingly suggests that environmental exposures early in development have a role in susceptibility to disease in later life. In addition, some of these environmental effects seem to be passed on through subsequent generations. Epigenetic modifications provide a plausible link between the environment and alterations in gene expression that might lead to disease phenotypes. An increasing body of evidence from animal studies supports the role of environmental epigenetics in disease susceptibility. Furthermore, recent studies have demonstrated for the first time that heritable environmentally induced epigenetic modifications underlie reversible transgenerational alterations in phenotype. Methods are now becoming available to investigate the relevance of these phenomena to human disease.

Small silencing RNAs: an expanding universe

Abstract: Since the discovery in 1993 of the first small silencing RNA, a dizzying number of small RNA classes have been identified, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). These classes differ in their biogenesis, their modes of target regulation and in the biological pathways they regulate. There is a growing realization that, despite their differences, these distinct small RNA pathways are interconnected, and that small RNA pathways compete and collaborate as they regulate genes and protect the genome from external and internal threats.

MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship

Abstract: MicroRNAs (miRNAs) have emerged as key gene regulators in diverse biological pathways. These small non-coding RNAs bind to target sequences in mRNAs, typically resulting in repressed gene expression. Several methods are now available for identifying miRNA target sites, but the mere presence of an miRNA-binding site is insufficient for predicting target regulation. Regulation of targets by miRNAs is subject to various levels of control, and recent developments have presented a new twist; targets can reciprocally control the level and function of miRNAs. This mutual regulation of miRNAs and target genes is challenging our understanding of the gene-regulatory role of miRNAs in vivo and has important implications for the use of these RNAs in therapeutic settings.