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Shotgun Cloning of Transposon Insertions in the Genome of Caenorhabditis elegans  [PDF]
Alexander M. van der Linden,Ronald H. A. Plasterk
Comparative and Functional Genomics , 2004, DOI: 10.1002/cfg.392
Abstract: We present a strategy to identify and map large numbers of transposon insertions in the genome of Caenorhabditis elegans. Our approach makes use of the mutator strain mut-7, which has germline-transposition activity of the Tc1/mariner family of transposons, a display protocol to detect new transposon insertions, and the availability of the genomic sequence of C. elegans. From a pilot insertional mutagenesis screen, we have obtained 351 new Tc1 transposons inserted in or near 219 predicted C. elegans genes. The strategy presented provides an approach to isolate insertions of natural transposable elements in many C. elegans genes and to create a large-scale collection of C. elegans mutants.
A Conserved Upstream Motif Orchestrates Autonomous, Germline-Enriched Expression of Caenorhabditis elegans piRNAs  [PDF]
Allison C. Billi equal contributor,Mallory A. Freeberg equal contributor,Amanda M. Day,Sang Young Chun,Vishal Khivansara,John K. Kim
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003392
Abstract: Piwi-interacting RNAs (piRNAs) fulfill a critical, conserved role in defending the genome against foreign genetic elements. In many organisms, piRNAs appear to be derived from processing of a long, polycistronic RNA precursor. Here, we establish that each Caenorhabditis elegans piRNA represents a tiny, autonomous transcriptional unit. Remarkably, the minimal C. elegans piRNA cassette requires only a 21 nucleotide (nt) piRNA sequence and an ~50 nt upstream motif with limited genomic context for expression. Combining computational analyses with a novel, in vivo transgenic system, we demonstrate that this upstream motif is necessary for independent expression of a germline-enriched, Piwi-dependent piRNA. We further show that a single nucleotide position within this motif directs differential germline enrichment. Accordingly, over 70% of C. elegans piRNAs are selectively expressed in male or female germline, and comparison of the genes they target suggests that these two populations have evolved independently. Together, our results indicate that C. elegans piRNA upstream motifs act as independent promoters to specify which sequences are expressed as piRNAs, how abundantly they are expressed, and in what germline. As the genome encodes well over 15,000 unique piRNA sequences, our study reveals that the number of transcriptional units encoding piRNAs rivals the number of mRNA coding genes in the C. elegans genome.
The Oogenic Germline Starvation Response in C. elegans  [PDF]
Hannah S. Seidel, Judith Kimble
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0028074
Abstract: Many animals alter their reproductive strategies in response to environmental stress. Here we have investigated how L4 hermaphrodites of Caenorhabditis elegans respond to starvation. To induce starvation, we removed food at 2 h intervals from very early- to very late-stage L4 animals. The starved L4s molted into adulthood, initiated oogenesis, and began producing embryos; however, all three processes were severely delayed, and embryo viability was reduced. Most animals died via ‘bagging,’ because egg-laying was inhibited, and embryos hatched in utero, consuming their parent hermaphrodites from within. Some animals, however, avoided bagging and survived long term. Long-term survival did not rely on embryonic arrest but instead upon the failure of some animals to produce viable progeny during starvation. Regardless of the bagging fate, starved animals showed two major changes in germline morphology: All oogenic germlines were dramatically reduced in size, and these germlines formed only a single oocyte at a time, separated from the remainder of the germline by a tight constriction. Both changes in germline morphology were reversible: Upon re-feeding, the shrunken germlines regenerated, and multiple oocytes formed concurrently. The capacity for germline regeneration upon re-feeding was not limited to the small subset of animals that normally survive starvation: When bagging was prevented ectopically by par-2 RNAi, virtually all germlines still regenerated. In addition, germline shrinkage strongly correlated with oogenesis, suggesting that during starvation, germline shrinkage may provide material for oocyte production. Finally, germline shrinkage and regeneration did not depend upon crowding. Our study confirms previous findings that starvation uncouples germ cell proliferation from germline stem cell maintenance. Our study also suggests that when nutrients are limited, hermaphrodites scavenge material from their germlines to reproduce. We discuss our findings in light of the recently proposed state of dormancy, termed Adult Reproductive Diapause.
Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs
Michelle Kudron, Wei Niu, Zhi Lu, Guilin Wang, Mark Gerstein, Michael Snyder, Valerie Reinke
Genome Biology , 2013, DOI: 10.1186/gb-2013-14-1-r5
Abstract: We determined the genome-wide binding profiles for Caenorhabditis elegans Rb/E2F-like components in the germline, in the intestine and broadly throughout the soma, and uncovered highly tissue-specific binding patterns and target genes. Chromatin association by LIN-35, the C. elegans ortholog of Rb, is impaired in the germline but robust in the soma, a characteristic that might govern differential effects on gene expression in the two cell types. In the intestine, LIN-35 and the heterochromatin protein HPL-2, the ortholog of Hp1, coordinately bind at many sites lacking E2F. Finally, selected direct target genes contribute to the soma-to-germline transformation of lin-35 mutants, including mes-4, a soma-specific target that promotes H3K36 methylation, and csr-1, a germline-specific target that functions in a 22G small RNA pathway.In sum, identification of tissue-specific binding profiles and effector target genes reveals important insights into the mechanisms by which Rb/E2F controls distinct cell fates in vivo.
The Caenorhabditis elegans HEN1 Ortholog, HENN-1, Methylates and Stabilizes Select Subclasses of Germline Small RNAs  [PDF]
Allison C. Billi,Amelia F. Alessi,Vishal Khivansara,Ting Han,Mallory Freeberg,Shohei Mitani,John K. Kim
PLOS Genetics , 2012, DOI: 10.1371/journal.pgen.1002617
Abstract: Small RNAs regulate diverse biological processes by directing effector proteins called Argonautes to silence complementary mRNAs. Maturation of some classes of small RNAs involves terminal 2′-O-methylation to prevent degradation. This modification is catalyzed by members of the conserved HEN1 RNA methyltransferase family. In animals, Piwi-interacting RNAs (piRNAs) and some endogenous and exogenous small interfering RNAs (siRNAs) are methylated, whereas microRNAs are not. However, the mechanisms that determine animal HEN1 substrate specificity have yet to be fully resolved. In Caenorhabditis elegans, a HEN1 ortholog has not been studied, but there is evidence for methylation of piRNAs and some endogenous siRNAs. Here, we report that the worm HEN1 ortholog, HENN-1 (HEN of Nematode), is required for methylation of C. elegans small RNAs. Our results indicate that piRNAs are universally methylated by HENN-1. In contrast, 26G RNAs, a class of primary endogenous siRNAs, are methylated in female germline and embryo, but not in male germline. Intriguingly, the methylation pattern of 26G RNAs correlates with the expression of distinct male and female germline Argonautes. Moreover, loss of the female germline Argonaute results in loss of 26G RNA methylation altogether. These findings support a model wherein methylation status of a metazoan small RNA is dictated by the Argonaute to which it binds. Loss of henn-1 results in phenotypes that reflect destabilization of substrate small RNAs: dysregulation of target mRNAs, impaired fertility, and enhanced somatic RNAi. Additionally, the henn-1 mutant shows a weakened response to RNAi knockdown of germline genes, suggesting that HENN-1 may also function in canonical RNAi. Together, our results indicate a broad role for HENN-1 in both endogenous and exogenous gene silencing pathways and provide further insight into the mechanisms of HEN1 substrate discrimination and the diversity within the Argonaute family.
Germline Signals Deploy NHR-49 to Modulate Fatty-Acid β-Oxidation and Desaturation in Somatic Tissues of C. elegans  [PDF]
Ramesh Ratnappan,Francis R. G. Amrit,Shaw-Wen Chen,Hasreet Gill,Kyle Holden,Jordan Ward,Keith R. Yamamoto,Carissa P. Olsen,Arjumand Ghazi
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004829
Abstract: In C. elegans, removal of the germline extends lifespan significantly. We demonstrate that the nuclear hormone receptor, NHR-49, enables the response to this physiological change by increasing the expression of genes involved in mitochondrial β-oxidation and fatty-acid desaturation. The coordinated augmentation of these processes is critical for germline-less animals to maintain their lipid stores and to sustain de novo fat synthesis during adulthood. Following germline ablation, NHR-49 is up-regulated in somatic cells by the conserved longevity determinants DAF-16/FOXO and TCER-1/TCERG1. Accordingly, NHR-49 overexpression in fertile animals extends their lifespan modestly. In fertile adults, nhr-49 expression is DAF-16/FOXO and TCER-1/TCERG1 independent although its depletion causes age-related lipid abnormalities. Our data provide molecular insights into how reproductive stimuli are integrated into global metabolic changes to alter the lifespan of the animal. They suggest that NHR-49 may facilitate the adaptation to loss of reproductive potential through synchronized enhancement of fatty-acid oxidation and desaturation, thus breaking down some fats ordained for reproduction and orchestrating a lipid profile conducive for somatic maintenance and longevity.
A statistical approach predicts human microRNA targets
Neil R Smalheiser, Vetle I Torvik
Genome Biology , 2004, DOI: 10.1186/gb-2004-5-2-p4
Abstract: We carried out a population-wide statistical analysis of how human microRNAs interact complementarily with human mRNAs present in the RefSeq database, looking for characteristics that differ significantly as compared with scrambled control sequences. These characteristics were used to predict a list of 72 candidate mRNA targets with 81% confidence. Unlike the case in C. elegans and Drosophila, many human microRNAs exhibited long exact matches (10 or more bases in a row), up to and including perfect target complementarity. Human microRNAs hit putative mRNA targets within the protein coding region about 2/3 of the time. And, microRNA hits in the candidate list did not have better complementarity near their 5'-end than expected by chance. In several cases, an individual microRNA hit multiple mRNAs that belonged to the same functional class.The candidate list predicts a significant number of well-known and novel human genes that warrant experimental validation as mRNA targets, including several that may be regulated by RNA interference. The list also provides a training set and suggests an unified model to assist prediction of mRNA targets that do not have especially long regions of target complementarity.Additional data files 1,2,3 and 4.
MicroRNA Predictors of Longevity in Caenorhabditis elegans  [PDF]
Zachary Pincus,Thalyana Smith-Vikos,Frank J. Slack
PLOS Genetics , 2011, DOI: 10.1371/journal.pgen.1002306
Abstract: Neither genetic nor environmental factors fully account for variability in individual longevity: genetically identical invertebrates in homogenous environments often experience no less variability in lifespan than outbred human populations. Such variability is often assumed to result from stochasticity in damage accumulation over time; however, the identification of early-life gene expression states that predict future longevity would suggest that lifespan is least in part epigenetically determined. Such “biomarkers of aging,” genetic or otherwise, nevertheless remain rare. In this work, we sought early-life differences in organismal robustness in unperturbed individuals and examined the utility of microRNAs, known regulators of lifespan, development, and robustness, as aging biomarkers. We quantitatively examined Caenorhabditis elegans reared individually in a novel apparatus and observed throughout their lives. Early-to-mid–adulthood measures of homeostatic ability jointly predict 62% of longevity variability. Though correlated, markers of growth/muscle maintenance and of metabolic by-products (“age pigments”) report independently on lifespan, suggesting that graceful aging is not a single process. We further identified three microRNAs in which early-adulthood expression patterns individually predict up to 47% of lifespan differences. Though expression of each increases throughout this time, mir-71 and mir-246 correlate with lifespan, while mir-239 anti-correlates. Two of these three microRNA “biomarkers of aging” act upstream in insulin/IGF-1–like signaling (IIS) and other known longevity pathways, thus we infer that these microRNAs not only report on but also likely determine longevity. Thus, fluctuations in early-life IIS, due to variation in these microRNAs and from other causes, may determine individual lifespan.
C. elegans rrf-1 Mutations Maintain RNAi Efficiency in the Soma in Addition to the Germline  [PDF]
Caroline Kumsta, Malene Hansen
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0035428
Abstract: Gene inactivation through RNA interference (RNAi) has proven to be a valuable tool for studying gene function in C. elegans. When combined with tissue-specific gene inactivation methods, RNAi has the potential to shed light on the function of a gene in distinct tissues. In this study we characterized C. elegans rrf-1 mutants to determine their ability to process RNAi in various tissues. These mutants have been widely used in RNAi studies to assess the function of genes specifically in the C. elegans germline. Upon closer analysis, we found that two rrf-1 mutants carrying different loss-of-function alleles were capable of processing RNAi targeting several somatically expressed genes. Specifically, we observed that the intestine was able to process RNAi triggers efficiently, whereas cells in the hypodermis showed partial susceptibility to RNAi in rrf-1 mutants. Other somatic tissues in rrf-1 mutants, such as the muscles and the somatic gonad, appeared resistant to RNAi. In addition to these observations, we found that the rrf-1(pk1417) mutation induced the expression of several transgenic arrays, including the FOXO transcription factor DAF-16. Unexpectedly, rrf-1(pk1417) mutants showed increased endogenous expression of the DAF-16 target gene sod-3; however, the lifespan and thermo-tolerance of rrf-1(pk1417) mutants were similar to those of wild-type animals. In sum, these data show that rrf-1 mutants display several phenotypes not previously appreciated, including broader tissue-specific RNAi-processing capabilities, and our results underscore the need for careful characterization of tissue-specific RNAi tools.
Probing the worm germline
Barry Lubarsky
Genome Biology , 2000, DOI: 10.1186/gb-2000-1-5-reports0073
Abstract: The authors constructed DNA microarrays containing almost 12,000 genes (63% of all those predicted to be present in the C. elegans genome). By hybridizing labeled RNA from a mutant in which all germ cells are absent to these arrays, and comparing the profiles obtained to similar hybridizations of wild-type RNA, they could determine which genes had significantly enriched transcript levels in the germline. Likewise, they compared RNA expression levels between two other mutants, one that produces only sperm and one that produces only oocytes (the worm is usually a hermaphrodite). In all, almost 12% (1,416) of the genes on the microarray were enriched in the germline. Among these were 650 genes enriched in sperm, 258 enriched in oocytes, and 508 genes expressed at similar levels in both mutant lines, suggesting that they are general factors required in the germ line. These experiments were repeated over a time span encompassing the last three larval stages and the adult animal. Sperm-enriched transcripts are present mostly in the final larval stage, whereas most oocyte and general germline genes are activated in the adult.The complete dataset from these microarray experiments can be found at the Kim lab website on the appropriate page - A global profile of germline gene expression in C. elegans.The sperm-enriched gene set included a large number of cytoplasmic protein kinases and phosphatases, reflecting the fact that most of sperm development involves post-translational events Enzymes required for fatty acid metabolism, to provide energy for mobility were also well-represented in the sperm-enriched gene set. The oocyte set included a large number of genes involved in DNA replication, early cell division, and embryonic patterning. Genes involved generally in the germline included those required for stem-cell maintenance, RNA metabolism, and RNA processing.Transcripts of almost all genes previously known to be involved in the worm germline were enriched in the germline a
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