Nature Cell Biology “News and Views” : RNA takes over control of DNA break repair

Francesca Storici and Ailone E. Tichon

Small RNAs generated at DNA break sites are implicated in mammalian DNA repair. Now, a study shows that following the formation of DNA double-strand breaks, bidirectional transcription events adjacent to the break generate small RNAs that trigger the DNA damage response by local RNA:RNA interactions.

Maintenance of DNA integrity is crucial for a cell to have a healthy life and for transmission of accurate genetic information to its progeny. Exogenous agents, including radiation or chemicals, as well as endogenous sources, such as reactive oxygen species or defects in DNA metabolism, pose threats to genome stability. Among the most dangerous DNA lesions are DNA double-strand breaks (DSBs), which if not properly and timely sealed can become sites of mutations or chromosomal rearrangements — well-known hallmarks of cancer and other genetic disorders1. The process of DSB repair is one of the most extensively studied mechanisms of DNA repair, yet much remains to be understood about its players and dynamics.
The DNA damage response (DDR) is a complex network of cellular pathways that detect DNA lesions and organize a response signal cascade to repair the DNA. In this issue of Nature Cell Biology, Michelini et al.2 uncover an aspect of the DDR in which RNAs are the directors. The study shows that sequencespecific RNA:RNA interactions orchestrate the DDR in response to DSBs.

Full text in pdf format.

News and Views pice in reference to the Walter Lab NCB paper (ref. 164 at https://sites.lsa.umich.edu/walter-lab/publications)

The drawing shows three different DNA DSB sites in a cell nucleus, depicted as interrupted, thick, parallel strands in blue, green and orange, respectively. The work by Michelini et al.2 suggests that every different DNA DSB site has its unique set of RNA:RNA interactions (shown as small, sandwiched, purple or red rectangles at the two DSB sites on the left) between its specific dilncRNAs and small non-coding RNAs termed DDRNAs (both shown as light blue, green or yellow lines), which originate from dilncRNAs at each DSB site. Such local RNA:RNA interactions are signals to activate the DDR by recruitment of the early DDR factor 53BP1 (transparent ovals). The dilncRNAs generated from DSB ends (thicker lines) were found to be more abundant than those generated towards DSB ends (thinner lines). ASOs can be designed to specifically block DSB repair at a chosen locus, without interfering with DSB repair at other loci within the same nucleus. Here, ASOs (shown as short, thick, brown lines) are specific to dilncRNA sequences of the DSB site on the right and block formation and function of DDRNAs at this DSB site by interacting (small, sandwiched, grey rectangles) with the complementary dilncRNAs.

Nature Reviews Research Highlight: DNA NANOTECHNOLOGY | Head over heels

Dynamic DNA nanotechnology enables the design of DNA-based nanomachines, such as molecular motors or nanorobots. However, most DNA nanomachines operate on a slow timescale, ranging from minutes to hours. Now, Nils Walter and colleagues, writing in Nature Nanotechnology, have made a single-stranded DNA walker that moves by performing cartwheels and at considerably faster speeds than previously reported DNA walkers.

Credit: Rachael Tremlett/Macmillan Publishers Limited

Read full research highlight in the journal Nature Reviews Materials : Head over heels

PDF version

 

Study finds snap-lock mechanism in bacterial riboswitch

Using single-molecule imaging, scientists from Rice University and the University of Michigan determined that the T-box riboswitch that regulates production of glycine in Bacillus subtilis becomes locked into the “on” position via a snap-lock mechanism. The lock is engaged when an L-shaped arm of uncharged tRNA snaps into position. When the arm is “charged” with a glycine molecule, the arm cannot lock into position, and the switch remains “off.” (Image courtesy of E. Nikonowicz/Rice University)

Finding by Rice, Michigan chemists could point way to new antibiotics
HOUSTON — (May 21, 2018) — In a discovery that points to potential new antibiotic medicines, scientists from Rice University and the University of Michigan have deciphered the workings of a common but little-understood bacterial switch that cuts off protein production before it begins.

Many gram-positive bacteria use T-box riboswitches to regulate production of proteins that utilize amino acids, the basic building blocks of all proteins. A study in Nature Communications describes how one of these switches, a glycine regulator in Bacillus subtilis, flips and locks into the “on” position via a snap-lock mechanism. Engaging the lock increases production of proteins that utilize glycine, the simplest amino acid. Researchers also detailed the switch’s “off” position: A single glycine at the tip of the locking arm blocks protein production.

 

Read full text here: Study finds snap-lock mechanism in bacterial riboswitch

Nature Research Highlight: Gymnastic feats help DNA ‘walker’ set speed record

A molecular motor flips end over end to cover 300 nanometres a minute.

A short segment of DNA anchors one end of itself and then flings the other end forward. Credit: Zhuoru Li

An acrobatic DNA segment that cartwheels across a surface is one of the fastest ‘walking’ molecules yet designed.

Researchers seeking to design nanorobots have synthesized DNA molecules that move autonomously. But most of these ‘walkers’ require several minutes to take a single step.

Nils Walter at the University of Michigan in Ann Arbor and his colleagues built a DNA walker that moves along a grid of ‘footholds’, which are made of complementary DNA building blocks called nucleotides. Each end of the walker has sequences of nucleotides that it uses to attach itself to the grid. Then it flips end over end to attach itself to another foothold.

The molecule can flip as many as 43 times per minute, covering a distance of 300 nanometres. This is an order of magnitude faster than the pace of other types of DNA walker.

Read full research highlight in the journal Nature : Gymnastic feats help DNA ‘walker’ set speed record

Tiny nanomachine successfully completes test drive

Researchers build a one-wheeled vehicle out of DNA rings

The two rings are linked like a chain and can well be recognized. At the centre there is the T7 RNA Polymerase.
Credit: Copyright Julián Valero

Scientists have used nanostructures to construct a tiny machine that constitutes a rotatory motor and can move in a specific direction. The researchers used circular structures from DNA.

Together with colleagues from the USA, scientists from the University of Bonn and the research institute Caesar in Bonn have used nanostructures to construct a tiny machine that constitutes a rotatory motor and can move in a specific direction. The researchers used circular structures from DNA. The results will now be presented in the journal Nature Nanotechnology.

Read full text here: Tiny nanomachine successfully completes test drive

Built for speed: DNA nanomachines take a (rapid) step forward

When it comes to matching simplicity with staggering creative potential, DNA may hold the prize. Built from an alphabet of just four nucleic acids, DNA provides the floorplan from which all earthly life is constructed.

Through a process known as strand displacement, a tiny walking device composed of DNA moves across a surface in a cartwheeling motion. The new device performed this feat more rapidly than any DNA walker designed to date. Credit: Nature Nanotechnology/Nils Walter

But DNA’s remarkable versatility doesn’t end there. Researchers have managed to coax segments of DNA into performing a host of useful tricks. DNA sequences can form logical circuits for nanoelectronic applications. They have been used to perform sophisticated mathematical computations, like finding the optimal path between multiple cities. And DNA is the basis for a new breed of tiny robots and nanomachines. Measuring thousands of times smaller than a bacterium, such devices can carry out a multitude of tasks.

In new research, Hao Yan of Arizona State University and his colleagues describe an innovative DNA walker, capable of rapidly traversing a prepared track. Rather than slow, tentative steps across a surface, the DNA acrobat cartwheels head over heels, covering ground 10- to 100-fold faster than previous devices.

“It is exciting to see that DNA walkers can increase their speed significantly by optimizing DNA strand length and sequences, the collaborative effort really made this happen,” Yan said.

Yan is the Milton D. Glick Distinguished Professor of Chemistry and Biochemistry at ASU and director of the Biodesign Center for Molecular Design and Biomimetics.

The study was led by Nils G. Walter, Francis S. Collins Collegiate Professor of Chemistry, Biophysics & Biological Chemistry, founding director of the Single Molecule Analysis in Real-Time (SMART) Center and founding co-director of the Center for RNA Biomedicine at the University of Michigan, and his team, along with collaborators from the Wyss Institute, the Dana Farber Cancer Institute and the Department of Biological Chemistry at Harvard (all in Boston, Massachusetts).

“The trick was to make the walker go head over heels, which is so much faster than the hopping used before—just as you would see in a kung fu action movie where the hero speeds up by cartwheeling to catch the villain,” says Walter.

The improvements in speed and locomotion displayed by the new walker should encourage further innovations in the field of DNA nanotechnology.

The group’s findings appear in the advanced online issue of the journal Nature Nanotechnology.

Read full text here: Building Motors to Drive Nanorobots

2015 Announcements

9/9/15

Congratulations to Dr. Paul Lund for successfully defending his thesis entitled ”Interactions between the translation machinery and a translational preQ1 riboswitch”!

3/19/15

Congratulations to Dr. Matthew Kahlscheuer for successfully defending his thesis entitled ”Characterization of pre-mRNA Dynamics and Structure throughout Spliceosome Assembly and Catalysis”!

2014 Announcements

9/01/14

A video highlight of Nils’s Presentation at Mcubed Symposium 2013 entitled “Seeing is Believing: Electron Microscopy and the Art of DNA Sushi” is now available online here.

8/15/14

Congratulations to Dr. Matthew Marek for successfully defending his thesis entitled “Heterogeneous folding and function of small RNA motifs: The hairpin ribozyme and a translational riboswitch”!

6/7/14

IMG_0355 copyIMG_0370RNAmeeting7

Congratulations to Matthew (Matt) Kahlscheuer for receiving the Nature Reviews Molecular Cell Biology best poster award at the RNA Society meeting 2014 in Quebec City! His award is featured in the Fall 2014 RNA Society Newsletter.

4/28/14

Congratulations to Dr. Wendy Tay for successfully defending her thesis entitled “Structures, Dynamics, and Ribozymes: An Investigation of RNA Structural Dynamics With the Hepatitis Delta Virus and Hairpin Ribozymes”!

3/8/14

Congratulations to Dr. Krishna Chaitanya Suddala for successfully defending his thesis entitled “A Tale of Two RNAs: Single Molecule Investigation of the Conformation, Dynamics and Ligand binding to the PreQ1 and T-box Riboswitches”!

3/22/14

Nils’s Presentation in the Saturday Morning Physics entitled “The Origin of Life: Chemistry As The Driver of Our Evolution” is now available online—video below.

3/10/14

Congratulations to Dr. Kamali Sripathi for successfully defending her thesis entitled “Structural Dynamics of the Hepatitis Delta Virus and Hairpin Ribozymes: Implications for Function”!

3/4/14

Congratulations to Matthew (Matt) Kahlscheuer for receiving the Travel Award for the RNA 2014 meeting!

2013 Announcements

10/28/13

Congratulations to Krishna Suddala for receiving the Rackham Graduate Student Research Grant!

8/2/13

Congratulations to Dr. Ramya Krishnan for successfully defending her thesis entitled “Understanding Pre-mRNA Dynamics in Single Spliceosome Complexes”!

7/16/13

Congratulations to Matthew (Matt) Kahlscheuer, Paul Lund, and Corey Custer for receiving the Rackham Graduate Student Research Grant!

5/10/13

Congratulations to Nils for receiving the Imes and Moore Faculty Award!

5/7/13

Congratulations to Dr. Vishalakshi Krishnan for successfully defending her thesis entitled “An Investigation of the RNA Induced Silencing Complex and its Therapeutic Implications”!

5/2/13

Congratulations to Dr. Arlie Rinaldi for successfully defending her thesis entitled “Establishing Ligand Mediated RNA Folding of Translational Riboswitches as Genetic Regulators using Single Molecule Microscopy”!

5/1/13

Congratulations to Dr. Nicole Michelotti for successfully defending her thesis entitled “Using Brownian Motion to Characterize the Nuclear Pore Complex, Molecular Robots, and Antimony-Doped Tin Oxide”!

4/19/13

Congratulations to Dr. Erika N. Cline for successfully defending her thesis entitled “Interactions between Nanoparticles and Biological Charged Lines: Biological Mimics of Protein-DNA Complexes and Microtubules as Drug Targets”!

4/18/13

Congratulations to Dr. Mario Reynaldo Blanco for successfully defending his thesis entitled “Splicing at Single Molecule Resolution: pre-mRNA Dynamics throughout Spliceosome Assembly and Catalysis”!

4/5/13

Congratulations to Mariusz who will be entering Johns Hopkin University’s Biophysics graduate program this fall!

3/22/13

Congratulations to Corey for receiving a 2013 GAANN fellowship!

3/15/13

Congratulations to Nils for receiving the University of Michigan Faculty Recognition Award!

3/15/13

Congratulations to Maria and Will for receiving Chemistry Summer Undergraduate Research Fellowships!

2012 Announcements

12/18/12

Congratulations to Dr. Alex Johnson-Buck for successfully defending his thesis entitled “Detection of Stochastic and Heterogeneous Behaviors in DNA Nanodevices by Super-resolution Fluorescence Microscopy”!

6/2/12

Congratulations to Arlie for receiving the NSMB poster award at the RNA Society Meeting (selected from over 450 posters)!

4/24/12

Congratulations to Wendy for receiving a Canadian NSERC predoctoral scholarship!

3/25/12

Congratulations to Sethu and Visha on their wedding day!

3/9/12

Congratulations to Alex for receiving the Outstanding Graduate Student Instructor Award!

2/22/12

Congratulations to Alex for receiving the highly competitive Rackham Predoctoral Fellowship! This fellowship supports outstanding doctoral students who have achieved candidacy and are actively working on dissertation research and writing.

2/8/12

Congratulations to Krishna and Surma on their wedding day!

12/20/11

Congratulations to Dr. Sethu(ramasundaram) Pitchiaya for successfully defending his thesis entitled “Probing microRNA Activity in vitro and inside Cells Using Single Molecule Microscopy”!

12/14/11

Congratulations to Dr. Gabrielle Todd for successfully defending her thesis entitled “Secondary Structure of Bacteriophage T4 Gene 60 mRNA: Implications for Translational Bypassing”!