Stage-specific combinations of opposing poly(A) modifying enzymes guide gene expression during early oogenesis

Abstract RNA-modifying enzymes targeting mRNA poly(A) tails are universal regulators of post-transcriptional gene expression programs. Current data suggest that an RNA-binding protein (RBP) directed tug-of-war between tail shortening and re-elongating enzymes operates in the cytoplasm to repress or activate specific mRNA targets. While this concept is widely accepted, it was primarily described in the final meiotic stages of frog oogenesis and relies molecularly on a single class of RBPs, i.e. CPEBs, the deadenylase PARN and cytoplasmic poly(A) polymerase GLD-2. Using the spatial and temporal resolution of female gametogenesis in the nematode C. elegans, we determined the distinct roles of known deadenylases throughout germ cell development and discovered that the Ccr4–Not complex is the main antagonist to GLD-2-mediated mRNA regulation. We find that the Ccr4–Not/GLD-2 balance is critical for essentially all steps of oocyte production and reiteratively employed by various classes of RBPs. Interestingly, its two deadenylase subunits appear to affect mRNAs stage specifically: while a Caf1/GLD-2 antagonism regulates mRNA abundance during all stages of oocyte production, a Ccr4/GLD-2 antagonism regulates oogenesis in an mRNA abundance independent manner. Our combined data suggests that the Ccr4–Not complex represents the evolutionarily conserved molecular opponent to GLD-2 providing an antagonistic framework of gene-specific poly(A)-tail regulation.

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CELF RNA binding proteins promote axon regeneration in C. elegans and mammals through alternative splicing of Syntaxins

eLife ◽

10.7554/elife.16072 ◽

2016 ◽

Vol 5 ◽

Cited By ~ 13

Author(s):

Lizhen Chen ◽

Zhijie Liu ◽

Bing Zhou ◽

Chaoliang Wei ◽

Yu Zhou ◽

...

Keyword(s):

Gene Expression ◽

Transcriptional Regulation ◽

Alternative Splicing ◽

Binding Proteins ◽

Rna Binding ◽

Axon Regeneration ◽

Rna Binding Proteins ◽

Mrna Isoforms ◽

C Elegans ◽

Mrna Targets

Axon injury triggers dramatic changes in gene expression. While transcriptional regulation of injury-induced gene expression is widely studied, less is known about the roles of RNA binding proteins (RBPs) in post-transcriptional regulation during axon regeneration. In C. elegans the CELF (CUGBP and Etr-3 Like Factor) family RBP UNC-75 is required for axon regeneration. Using crosslinking immunoprecipitation coupled with deep sequencing (CLIP-seq) we identify a set of genes involved in synaptic transmission as mRNA targets of UNC-75. In particular, we show that UNC-75 regulates alternative splicing of two mRNA isoforms of the SNARE Syntaxin/unc-64. In C. elegans mutants lacking unc-75 or its targets, regenerating axons form growth cones, yet are deficient in extension. Extending these findings to mammalian axon regeneration, we show that mouse Celf2 expression is upregulated after peripheral nerve injury and that Celf2 mutant mice are defective in axon regeneration. Further, mRNAs for several Syntaxins show CELF2 dependent regulation. Our data delineate a post-transcriptional regulatory pathway with a conserved role in regenerative axon extension.

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Polycombs and microRNA-223 regulate human granulopoiesis by transcriptional control of target gene expression

Blood ◽

10.1182/blood-2011-08-371344 ◽

2012 ◽

Vol 119 (17) ◽

pp. 4034-4046 ◽

Cited By ~ 101

Author(s):

Giuseppe Zardo ◽

Alberto Ciolfi ◽

Laura Vian ◽

Linda M. Starnes ◽

Monia Billi ◽

...

Keyword(s):

Gene Expression ◽

Dna Sequences ◽

Transcriptional Control ◽

Transcriptional Level ◽

Seed Region ◽

Mrna Targets ◽

Epigenetic Events ◽

Evolutionarily Conserved ◽

Lineage Decision ◽

Chromatin Remodeling Complexes

Abstract Epigenetic modifications regulate developmental genes involved in stem cell identity and lineage choice. NFI-A is a posttranscriptional microRNA-223 (miR-223) target directing human hematopoietic progenitor lineage decision: NFI-A induction or silencing boosts erythropoiesis or granulopoiesis, respectively. Here we show that NFI-A promoter silencing, which allows granulopoiesis, is guaranteed by epigenetic events, including the resolution of opposing chromatin “bivalent domains,” hypermethylation, recruitment of polycomb (PcG)–RNAi complexes, and miR-223 promoter targeting activity. During granulopoiesis, miR-223 localizes inside the nucleus and targets the NFI-A promoter region containing PcGs binding sites and miR-223 complementary DNA sequences, evolutionarily conserved in mammalians. Remarkably, both the integrity of the PcGs-RNAi complex and DNA sequences matching the seed region of miR-223 are required to induce NFI-A transcriptional silencing. Moreover, ectopic miR-223 expression in human myeloid progenitors causes heterochromatic repression of NFI-A gene and channels granulopoiesis, whereas its stable knockdown produces the opposite effects. Our findings indicate that, besides the regulation of translation of mRNA targets, endogenous miRs can affect gene expression at the transcriptional level, functioning in a critical interface between chromatin remodeling complexes and the genome to direct fate lineage determination of hematopoietic progenitors.

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Temporal Transcriptomics of Gut Escherichia coli in Caenorhabditis elegans Models of Aging

Microbiology Spectrum ◽

10.1128/spectrum.00498-21 ◽

2021 ◽

Author(s):

Joshua D. Brycki ◽

Jeremy R. Chen See ◽

Gillian R. Letson ◽

Cade S. Emlet ◽

Lavinia V. Unverdorben ◽

...

Keyword(s):

Gene Expression ◽

Escherichia Coli ◽

Caenorhabditis Elegans ◽

Life Span ◽

Wild Type ◽

Health Span ◽

Content Type ◽

C Elegans ◽

Evolutionarily Conserved

Previous research has reported effects of the microbiome on health span and life span of Caenorhabditis elegans , including interactions with evolutionarily conserved pathways in humans. We build on this literature by reporting the gene expression of Escherichia coli OP50 in wild-type (N2) and three long-lived mutants of C. elegans .

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Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises

Frontiers in Microbiology ◽

10.3389/fmicb.2020.624830 ◽

2021 ◽

Vol 11 ◽

Author(s):

Mikel Irastortza-Olaziregi ◽

Orna Amster-Choder

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Small Rnas ◽

Rna Binding ◽

Rna Binding Proteins ◽

Rna Localization ◽

Molecular Architecture ◽

Independent Manner ◽

New Information ◽

Shed Light

Coupled transcription-translation (CTT) is a hallmark of prokaryotic gene expression. CTT occurs when ribosomes associate with and initiate translation of mRNAs whose transcription has not yet concluded, therefore forming “RNAP.mRNA.ribosome” complexes. CTT is a well-documented phenomenon that is involved in important gene regulation processes, such as attenuation and operon polarity. Despite the progress in our understanding of the cellular signals that coordinate CTT, certain aspects of its molecular architecture remain controversial. Additionally, new information on the spatial segregation between the transcriptional and the translational machineries in certain species, and on the capability of certain mRNAs to localize translation-independently, questions the unanimous occurrence of CTT. Furthermore, studies where transcription and translation were artificially uncoupled showed that transcription elongation can proceed in a translation-independent manner. Here, we review studies supporting the occurrence of CTT and findings questioning its extent, as well as discuss mechanisms that may explain both coupling and uncoupling, e.g., chromosome relocation and the involvement of cis- or trans-acting elements, such as small RNAs and RNA-binding proteins. These mechanisms impact RNA localization, stability, and translation. Understanding the two options by which genes can be expressed and their consequences should shed light on a new layer of control of bacterial transcripts fate.

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KH domain containing RNA-binding proteins coordinate with microRNAs to regulate Caenorhabditis elegans development

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab013 ◽

2021 ◽

Vol 11 (2) ◽

Author(s):

Dustin Haskell ◽

Anna Zinovyeva

Keyword(s):

Gene Expression ◽

Caenorhabditis Elegans ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Regulate Gene Expression ◽

C Elegans ◽

Binding Domains ◽

Kh Domain ◽

Regulate Gene

Abstract MicroRNAs (miRNAs) and RNA-binding proteins (RBPs) regulate gene expression at the post-transcriptional level, but the extent to which these key regulators of gene expression coordinate their activities and the precise mechanisms of this coordination are not well understood. RBPs often have recognizable RNA binding domains that correlate with specific protein function. Recently, several RBPs containing K homology (KH) RNA binding domains were shown to work with miRNAs to regulate gene expression, raising the possibility that KH domains may be important for coordinating with miRNA pathways in gene expression regulation. To ascertain whether additional KH domain proteins functionally interact with miRNAs during Caenorhabditis elegans development, we knocked down twenty-four genes encoding KH-domain proteins in several miRNA sensitized genetic backgrounds. Here, we report that a majority of the KH domain-containing genes genetically interact with multiple miRNAs and Argonaute alg-1. Interestingly, two KH domain genes, predicted splicing factors sfa-1 and asd-2, genetically interacted with all of the miRNA mutants tested, whereas other KH domain genes showed genetic interactions only with specific miRNAs. Our domain architecture and phylogenetic relationship analyses of the C. elegans KH domain-containing proteins revealed potential groups that may share both structure and function. Collectively, we show that many C. elegans KH domain RBPs functionally interact with miRNAs, suggesting direct or indirect coordination between these two classes of post-transcriptional gene expression regulators.

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FACT sets a barrier for cell fate reprogramming inC. elegansand Human

10.1101/185116 ◽

2017 ◽

Cited By ~ 1

Author(s):

Ena Kolundzic ◽

Andreas Ofenbauer ◽

Bora Uyar ◽

Anne Sommermeier ◽

Stefanie Seelk ◽

...

Keyword(s):

Gene Expression ◽

Cell Fate ◽

Chromatin Accessibility ◽

Genetic Screen ◽

Cellular Reprogramming ◽

Stable Gene ◽

C Elegans ◽

Chromatin Regulator ◽

Evolutionarily Conserved ◽

Stable Gene Expression

The chromatin regulator FACT (Facilitates Chromatin Transcription) is essential for ensuring stable gene expression by promoting transcription. In a genetic screen usingC. eleganswe identified that FACT maintains cell identities and acts as a barrier for transcription factor-mediated cell fate reprogramming. Strikingly, FACTs role as a reprogramming barrier is conserved in humans as we show that FACT depletion enhances reprogramming of fibroblasts into stem cells and neurons. Such activity of FACT is unexpected since known reprogramming barriers typically repress gene expression by silencing chromatin. In contrast, FACT is a positive regulator of gene expression suggesting an unprecedented link of cell fate maintenance with counteracting alternative cell identities. This notion is supported by ATAC-seq analysis showing that FACT depletion results in decreased but also increased chromatin accessibility for transcription factors. Our findings identify FACT as a cellular reprogramming barrier inC. elegansand in Human, revealing an evolutionarily conserved mechanism for cell fate protection.

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Binding of an X-specific condensin correlates with a reduction in active histone modifications at gene regulatory elements

10.1101/516419 ◽

2019 ◽

Author(s):

Lena Annika Street ◽

Ana Karina Morao ◽

Lara Heermans Winterkorn ◽

Chen-Yu Jiao ◽

Sarah Elizabeth Albritton ◽

...

Keyword(s):

Gene Expression ◽

Histone Modifications ◽

Protein Complexes ◽

Regulatory Elements ◽

Chromosomal Gene ◽

Direct Link ◽

C Elegans ◽

Evolutionarily Conserved ◽

Gene Regulatory Elements ◽

Gene Regulatory

ABSTRACTCondensins are evolutionarily conserved protein complexes that are required for chromosome segregation during cell division and genome organization during interphase. In C. elegans,, a specialized condensin, which forms the core of the dosage compensation complex (DCC), binds to and represses X chromosome transcription. Here, we analyzed DCC localization and the effect of DCC depletion on histone modifications, transcription factor binding, and gene expression using ChIP-seq and mRNA-seq. Across the X, DCC accumulates at accessible gene regulatory sites in active chromatin and not heterochromatin. DCC is required for reducing the levels of activating histone modifications, including H3K4me3 and H3K27ac, but not repressive modification H3K9me3. In X-to-autosome fusion chromosomes, DCC spreading into the autosomal sequences locally reduces gene expression, thus establishing a direct link between DCC binding and repression. Together, our results indicate that DCC-mediated transcription repression is associated with a reduction in the activity of X chromosomal gene regulatory elements.SUMMARYCondensins are evolutionarily conserved protein complexes that mediate chromosome condensation during cell division and have been implicated in gene regulation during interphase. Here, we analyzed the gene regulatory role of an X-specific condensin (DCC) in C. elegans, by measuring its effect on histone modifications associated with transcription regulation. We found that in X-to-autosome fusion chromosomes, DCC spreading into autosomal sequences locally reduces gene expression, establishing a direct link between DCC binding and repression. DCC is required for reduced levels of histone modifications associated with transcription activation at X chromosomal promoters and enhancers. These results are consistent with a model whereby DCC binding directly or indirectly results in a reduction in the activity of X chromosomal gene regulatory elements through specific activating histone modifications.

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Translational control in the C. elegans hermaphrodite germ line

Genome ◽

10.1139/g09-090 ◽

2010 ◽

Vol 53 (2) ◽

pp. 83-102 ◽

Cited By ~ 9

Author(s):

Hilary Racher ◽

Dave Hansen

Keyword(s):

Gene Expression ◽

Cell Fate ◽

Translational Control ◽

Translational Regulation ◽

Developmental Stages ◽

Germ Line ◽

Control Of Gene Expression ◽

Cell Fate Decisions ◽

C Elegans ◽

Mrna Targets

The formation of a fully developed gamete from an undifferentiated germ cell requires progression through numerous developmental stages and cell fate decisions. The precise timing and level of gene expression guides cells through these stages. Translational regulation is highly utilized in the germ line of many species, including Caenorhabditis elegans , to regulate gene expression and ensure the proper formation of gametes. In this review, we discuss some of the developmental stages and cell fate decisions involved in the formation of functional gametes in the C. elegans germ line in which translational control has been implicated. These stages include the mitosis versus meiosis decision, the sperm/oocyte decision, and gamete maturation. We also discuss some of the techniques used to identify mRNA targets; the identification of these targets is necessary to clearly understand the role each RNA-binding protein plays in these decisions. Relatively few mRNA targets have been identified, thus providing a major focus for future research. Finally, we propose some reasons why translational control may be utilized so heavily in the germ line. Given that many species have this substantial reliance on translational regulation for the control of gene expression in the germ line, an understanding of translational regulation in the C. elegans germ line is likely to increase our understanding of gamete formation in general.

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Pat1 proteins: regulating mRNAs from birth to death?

BioMolecular Concepts ◽

10.1515/bmc-2012-0005 ◽

2012 ◽

Vol 3 (4) ◽

pp. 295-306

Author(s):

Nancy Standart ◽

Aline Marnef

Keyword(s):

Gene Expression ◽

Mammalian Cells ◽

Mrna Decay ◽

Rna Binding ◽

Rna Binding Proteins ◽

Viral Gene Expression ◽

Model Systems ◽

Viral Gene ◽

Nuclear Speckles ◽

Mrna Targets

AbstractThe Pat1 protein family has been the subject of several recent extensive investigations of diverse model systems ranging from yeast, flies and worms to man, using a variety of experimental approaches. Although some contradictions remain, the emerging consensus view is that these RNA-binding proteins act in mRNA decay by physically linking deadenylation with decapping and by regulating gene expression as translational repressors. These multiple functions are present in the single invertebrate Pat1 proteins, whereas, in vertebrates, one Pat1 variant represses translation in early development, while a somatic version synthesised in embrogenesis and in adults acts in mRNA decay. At steady state, Pat1 proteins are found enriched in cytoplasmic P(rocessing)-bodies, and related mRNP complexes and granules. Evidence recently obtained from mammalian tissue culture cells shows that Pat1 shuttles in and out of the nucleus, where it localises to nuclear speckles, PML bodies and nucleolar caps, which suggests RNA-related nuclear functions. Less well understood, Pat1 proteins may play additional roles in miRNA silencing and/or biogenesis, as well in the regulation of viral gene expression. Due to the relatively low level of sequence conservation between Pat1 proteins from different species and lacking any discernable motifs, determining their functional domains has proved difficult, as is obtaining a simple unified view of the location of the binding sites of their interacting proteins in all examined species. Questions that remain to be addressed include the following: 1) What are their roles in the nucleus? 2) What is the link, if one exists, between their cytoplasmic and nuclear roles? 3) Do they have specific mRNA targets? 4) Which signalling pathways regulate their P-body localisation in mammalian cells, which may affect quiescent cell survival?

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KH domain containing RNA-binding proteins coordinate with microRNAs to regulate Caenorhabditis elegans development

10.1101/2020.08.03.235127 ◽

2020 ◽

Author(s):

D Haskell ◽

A Zinovyeva

Keyword(s):

Gene Expression ◽

Caenorhabditis Elegans ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Regulate Gene Expression ◽

C Elegans ◽

Binding Domains ◽

Kh Domain ◽

Regulate Gene

ABSTRACTmicroRNAs (miRNAs) and RNA binding proteins (RBPs) regulate gene expression at the post-transcriptional level, but the extent to which these key regulators of gene expression coordinate and the precise mechanisms of their coordination are not well understood. RNA binding proteins often have recognizable RNA binding domains that correlate with specific protein function. Recently, several RBPs containing K Homology (KH) RNA binding domains were shown to work with miRNAs to regulate gene expression, raising the possibility that KH domains may be important for coordinating with miRNA pathways in gene expression regulation. To ascertain whether additional KH domain proteins functionally interact with miRNAs during Caenorhabditis elegans development, we knocked down twenty-four genes encoding KH-domain proteins in several miRNA sensitized genetic backgrounds. Here, we report that a majority of the KH domain-containing genes genetically interact with multiple miRNAs and Argonaute alg-1. Interestingly, two KH domain genes, predicted splicing factors sfa-1 and asd-2, genetically interacted with all of the miRNA mutants tested, while other KH domain genes exhibited functional interactions only with specific miRNAs. Our domain architecture and phylogenetic relationship analyses of the C. elegans KH domain-containing proteins revealed potential groups that may share both structure and function. Collectively, we show that many C. elegans KH domain RBPs functionally interact with miRNAs, suggesting direct or indirect coordination between these two classes of post-transcriptional gene expression regulators.

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