Changing where the polyA tail is added to an mRNA transcript can fine-tune the tissue-specific expression of many genes, reports a Caenorhabditis elegans study published in the June issue of GENETICS. Blazie et al. show alternative polyadenylation (APA) allows transcripts to evade microRNA (miRNA) silencing in some tissues, allowing for tissue-specific expression of those genes. In a thorough study of transcription in eight different tissues, APA stands out as a widespread and previously unappreciated way to regulate genes that are expressed in multiple tissues.

APA occurs after an mRNA is transcribed. Before the transcript can be translated, it must be processed, which includes the addition of a run of adenine bases as the “tail.” Sometimes, post-transcriptional changes to mRNA processing can result in a different protein product or a different expression pattern. Alternative polyadenylation (APA) is a kind of post-transcriptional modification that changes the length of the 3’ untranslated region (UTR) by adding the poly-A tail to an alternative site in the transcript.

The authors obtained the tissue-specific transcriptome of five different C. elegans somatic tissues using a technique called PAT-Seq, which isolates transcripts from a target tissue by expressing a tagged poly-A binding protein in a tissue-specific pattern. PAT-Seq also allows for the precise detection of APA. Combined with previous transcriptome data from three other somatic tissues, this dataset represents the most thorough collection yet of tissue-specific mRNAs in C. elegans, accounting for the tissue-specific expression dynamics of nearly 60% of all annotated protein-coding genes.

Blazie et al. found evidence of APA in all eight somatic tissues they examined—most notably in genes that were expressed in all eight types. Shortening the 3’UTR can have important biological consequences because that is where miRNA target sites are usually found. These short, non-coding RNAs bind to complementary sequences in mRNAs and trigger a pathway that represses the bound transcript. Tissue-specific APA that shortens the 3’UTR and eliminates these miRNA targeting sites releases this regulation and allows translation to occur. Though many of the APA-regulated genes are expressed in multiple tissues, this post-transcriptional modification restricts their biological effect. On average, ubiquitously transcribed genes had longer 3’UTRs enriched with miRNA target sites, and APA eliminates an estimated 37% of these targets.

A closer analysis of the genes rack-1 and tct-1 provides an example—these two genes escape miRNA repression through APA leading to a shorter 3’UTR in muscle tissue. The authors used fluorescently tagged transcripts to show that those with shorter 3’UTRs were not repressed by miRNA in muscle tissue. Knocking down the expression of these genes in muscle tissue also caused embryonic lethality, suggesting that this process is an important regulatory mechanism for development.

Scientists have long known about APA in many organisms, but its significance has not been clear. The development of specific tissue and cell types requires a dynamic genome with multiple layers of gene, transcript, and protein regulation. Not only does this study provide a new resource for future investigation of tissue-specific transcript behavior, it also highlights APA as a regulatory mechanism with widespread consequences.

 

Blazie, S. M., Geissel, H. C., Wilky, H., Joshi, R., Newbern, J., & Mangone, M. (2017). Alternative Polyadenylation Directs Tissue Specific miRNA Targeting in Caenorhabditis elegans Somatic Tissues. GENETICS, 206(2): 757-774. DOI:10.1534/genetics.116.196774

http://www.genetics.org/content/206/2/757

 

Khraiwesh, B. & Salehi-Ashtiani, K. (2017). Commentary: Alternative Poly(A) Tails Meet miRNA Targeting in Caenorhabditis elegans. GENETICS, 206(2): 755-756. DOI:10.1534/genetics.117.202101

http://www.genetics.org/content/206/2/755

, , , ,

Katie is a science writer at GSA. She did her PhD work on the evolutionary consequences of genetic conflict in fruit flies at the University of Georgia.

View all posts by Katie Pieper »

Read more in

  • Collage of 2021 Rosalind Franklin Award recipients

    Where are they now? Rosalind Franklin Young Investigator Award recipients share updates on their research

    Rosalind Franklin Young Investigator Award applications are open–make sure you submit your application or nomination of a colleague by September 30, 2024.

  • University of Minnesota researchers map genome of the last living wild horse species

    The study, published in G3: Genes|Genomes|Genetics, is part of larger conservation efforts to save Przewalski’s horse.

  • Congratulations to the Spring 2024 DeLill Nasser Awardees!

    GSA is pleased to announce the recipients of the DeLill Nasser Award for Professional Development in Genetics for Spring 2024! Given twice a year to graduate students and postdoctoral researchers, DeLill Nasser Awards support attendance at meetings and laboratory courses. The award is named in honor of DeLill Nasser, a long-time GSA supporter and National Science Foundation…

  • Carolyn Damilola headshot

    Carolyn Damilola: an NFS Rising Scientist on a lifelong quest to learn more

    Carolyn Damilola is an NFS Rising Scientist from Nigeria doing respiratory system research and paving the way for scientists from underrepresented communities through mentorship.

  • Text over a blue background image: Apply for up to $2,000 for your project from the Starter Culture Microgrant Program.

    What does a good microgrant proposal look like?

    Members of the Microgrant Review Committee share their tips for a successful proposal.

  • A blurred image of a human face is shown against a dark background.

    The first piece of the facial recognition puzzle

    New research in GENETICS gives a first peek at the molecular pathway involved in recognizing faces.

  • New Senior Editor Amy MacQueen joins GENETICS

    A new senior editor is joining GENETICS in the Genome Integrity and Transmission section. We’re excited to welcome Amy MacQueen to the editorial team.

  • Close up of an adult zebrafish with blue and white stripes in an aquarium with red lighting.

    Block party on the zebrafish sex chromosome

    Research in G3 identifies a gene regulatory block of the zebrafish genome responsible for overseeing the maternal-to-zygotic-transition.

  • Lemna Minor, the common duckweed

    Unraveling the mysteries of duckweed: epigenetic insights from Spirodela polyrhiza

    Research published in G3 offers insight into the impact of DNA methylation on clonal propagation in asexually reproducing plants.

  • Luciano Marraffini headshot

    A microbiologist’s quest to understand CRISPR in bacterial self-defense

    2024 Genetics Society of America Medal recipient Luciano Marraffini determined how CRISPR-Cas systems destroy genetic targets with precision, paving the way for gene editing technology development.

  • Elaine Ostrander headshot

    Unlocking mysteries of trait and disease heritability in dogs

    2024 Edward Novitski Prize recipient Elaine Ostrander, a pioneer of the domestic dog model, discovered numerous genes affecting dog size, morphology, behavior, and disease susceptibility—many of which have relevance in humans.

  • NSF-funded BIO-LEAPS Grant to Support Culture Change in Genetics

    GSA and collaborators Personal Genetics Education & Dialogue and Reclaiming STEM Institute launch NSF-funded BIO-LEAPS project to support culture change in genetics 

    We are thrilled to announce that the Genetics Society of America (GSA) is collaborating with the Personal Genetics Education & Dialogue (PGED) based in the Department of Genetics at Harvard Medical School, and the Reclaiming STEM Institute (RSI) on a Leading Culture Change Through Professional Societies of Biology (BIO-LEAPS) grant from the U.S. National Science…

  • Daman Saluja: Navigating Science and Policy in India

    In the Paths to Science Policy series, we talk to individuals who have a passion for science policy and are active in advocacy through their various roles and careers. The series aims to inform and guide early career scientists interested in science policy. This series is brought to you by the GSA Early Care­er Scientist…

  • Deborah Andrew headshot

    A fly geneticist’s journey into discovering rules of organ development

    2024 George W. Beadle Award recipient Deborah Andrew discovered new genes and pathways in Drosophila salivary gland organogenesis. Now, her work can help optimize cell secretion in therapeutic applications and fight malaria.

  • Małgorzata Gazda's headshot

    Małgorzata Gazda: How receiving the DeLill Nasser Award helped her land her dream job

    Have you ever experienced an event that changes the course of your life, or in this case, your career? Małgorzata (Gosia) Gazda is Assistant Professor at the University of Montreal and in 2022, she received the DeLill Nasser Award for Professional Development in Genetics, which she used to attend and present at the 2022 Population,…

  • Hongyu Zhao joins GENETICS as new Senior Editor

    A new senior editor is joining GENETICS in the Statistical Genetics and Genomics section. We’re excited to welcome Hongyu Zhao to the editorial team.

  • Julio Molina Pineda at TAGC 2024

    GSA Member Julio Molina Pineda Receives DeLill Nasser Award, Shines at TAGC 2024 

    “At any career stage, the GSA membership is an amazing investment for any genetics professional!” Julio Molina Pineda is a PhD Candidate in Cell and Molecular Biology and a Research Assistant at the University of Arkansas, and a Doctoral Academy Fellow at the Lewis Lab. In 2023, Julio was awarded the DeLill Nasser Award for…

  • Ed Grell at his dissecting microscope using ether to anesthetize his flies.

    In Memoriam: Ellsworth Herman Grell (1932–2023), a pioneer of Drosophila genome engineering and annotation

    Ellsworth (Ed) Grell blessed the Drosophila community through three enduring legacies: as a pioneer of chromosome mechanics, as a primary organizer and synthesizer of genetic knowledge in Drosophila, and as a graceful mentor to those fortunate to have known him personally. Ed grew up in rural Nebraska, completed his undergraduate studies at Iowa State, and…

  • Congratulations to the #Fungal24 Poster Award winners!

    We are pleased to announce the recipients of the GSA Poster Awards for posters presented at the 32nd Fungal Genetics Conference! Undergraduate and graduate student members of GSA were eligible for the awards, and a hard-working team of judges made the determinations. Congratulations to all! Felicia Ebot Ojong, The University of Georgia My research is focused…

  • Poster presentation tips for TAGC 2024

    You’ve been selected to present a poster at The Allied Genetics Conference 2024 in March—you’ve celebrated, made plans to attend, now what? This is an exciting opportunity to showcase your research and engage with fellow members of the genetics community, so you want to make sure you’re prepared. We wanted to offer you some tips…

  • Maximize your TAGC 2024 experience 

    A guide to all that National Harbor & DC have to offer Are you joining us for The Allied Genetics Conference 2024 in March? Make the most of your #TAGC24 experience in National Harbor! We know the science will keep you busy, but you deserve to unwind and have some fun, so we’ve curated a…

  • Early Career Leadership Spotlight: Sarah Petrosky

    We’re taking time to get to know the members of the GSA’s Early Career Scientist Committees. Join us to learn more about our early career scientist advocates. Sarah PetroskyMultimedia SubcommitteeUniversity of Pittsburgh Research Interest I am interested in understanding adaptation that has been happening recently in populations by dissecting the ways that genes underlying an adaptation…

  • TAGC 2024 Early Career Award Winners

    GSA is pleased to announce the winners of the early career awards presented at The Allied Genetics Conference 2024. These awards are specific to particular TAGC communities and recognize early career scientists’ outstanding work on their respective research organisms. The awardees will present their talks in keynote sessions at TAGC 2024.  Don’t miss the opportunity…

  • Preeminent geneticists recognized with revamped GSA Awards

    In 2022, GSA’s Board of Directors launched an audit to review the five major awards conferred by the Society. Today, we are thrilled to announce the recipients of the reimagined GSA Awards, including the new Genetics Society of America Early Career Medal. The scientists honored this year are recognized by their peers for their outstanding…

  • Fly Board funds outreach programs to spread the word about Drosophila research

    In 2020, the Fly Board voted to use part of its reserve fund to support efforts to increase trainee participation as well as equity and diversity in the Drosophila community. An awards committee decides how the money will be spent each year, and from 2020–2022, the committee posted a very broad call for applications from…

  • New members of the GSA Board of Directors: 2024–2026

    We are pleased to announce the election of four new leaders to the GSA Board of Directors: 2024 Vice President/2025 President Brenda Andrews Professor, University of Toronto It’s an honor to continue my association with the Society by serving as Vice President of the Board of Directors. I have broad knowledge of the ongoing activities…

  • The Fly Meeting is one-of-a-kind! Dros 2025 organizers share their excitement

    The 66th Annual Drosophila Research Conference promises to be a meeting rich with the latest in Drosophila research as well as opportunities to advance your career and connect with a global community of 1,400+ scientists. The organizers Todd Nystul, Michelle Bland, Leila Rieder, Amanda Crocker, and Justin Crocker are hard at work, planning a conference…

  • Early Career Leadership Spotlight: Olufemi Osonowo

    We’re taking time to get to know the members of the GSA’s Early Career Scientist Committees. Join us to learn more about our early career scientist advocates. Olufemi Adekunle OsonowoCareer Development SubcommitteeDalhousie University Research Interest Metabolomics and genomics are two distinct but complimentary approaches that offer valuable insights into the underlying mechanisms of complex traits, such…

  • Early Career Leadership Spotlight: Hector Mendoza

    We’re taking time to get to know the members of the GSA’s Early Career Scientist Committees. Join us to learn more about our early career scientist advocates. Hector MendozaCommunication and Outreach SubcommitteeUniversity of Michigan Research Interest My research goals converge around the evolution of sexual reproduction. During my doctoral program, I investigated mitochondrial inheritance, a mechanism…