Nav: Home

New RNA mapping technique shows how RNA interacts with chromatin in the genome

February 25, 2020

A group led by scientists from the RIKEN Center for Integrative Medical Sciences (IMS) in Japan have developed a new method, RADICL-seq, which allows scientists to better understand how RNA interacts with the genome through chromatin--the structure in which the genome is organized.

There have been many changes in our understanding of the function of RNA in biology. Decades ago, it was generally believed that RNA functioned merely as an intermediary for the translation of DNA into proteins. However, the decoding of the human genome in the early 2000s led to the realization that a large amount of RNA--known as "junk" at the time--did not code proteins. Subsequent work on large-scale genomic projects such as ENCODE and RIKEN-led FANTOM found that there were large numbers of long non-protein coding RNAs in the mammalian genome, which interact with the DNA. Many of these RNAs are found in the cell nucleus, and are attached to chromatin, the structure used to tightly fold the DNA. However, it is still not clear exactly what RNAs interact with which regions of the DNA in different cells.

To achieve a better understanding of these interactions, and to determine whether RNA is actually a part of the chromatin structure, the scientists developed a new technology, which they called RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq), which maps genome-wide RNA-chromatin interactions in intact nuclei. This technology, published in Nature Communications, allows researchers to identify distinct patterns of genome occupancy for different classes of transcripts as well as cell type-specific RNA-chromatin interactions, and emphasizes the role of transcription in the establishment of chromatin structure.

To test the validity of the method, the scientists looked at two non-coding RNAs which are known to be expressed preferentially in certain cell types. The first, known at NEAT1, may be involved in the structure as it is associated with a mysterious structure known as paraspeckles found in mammalian cell nuclei. The second, Fgfr2, is involved in embryonic development and tissue repair, especially for bone and blood vessels. They found that in mouse embryonic stem cells--an early type of cell--that NEAT1 acts almost exclusively on genomic regions of chromosome 19, from which it itself derives from, whereas in oligodendrocyte progenitor cells--a later type of developmental cell that can differentiate into brain cells--it interacts with a broad range of genomic regions on other chromosomes as well. Fgfr2, by contrast, mostly interacts with genomic regions on its own chromosome.

"This study is a first step toward understanding how the interplay between RNA and chromatin ensures proper genome function. Our data indicate that RNAs may exert more widespread effects on gene regulation and chromatin organization than previously thought," says Alessandro Bonetti, one of the corresponding authors of the study.

"The broad, genome-wide applications of this technology will help us to understand the fundamental role of non-coding RNA as a regulator of genome activity, which could lead to future applications and therapies" says Piero Carninci, one of the senior authors of the study.
-end-
The work was done by scientists from RIKEN IMS along with scientists from Karolinska Institutet (Sweden), McGill University (Canada), Fondazione Santa Lucia (Italy), KAUST (Saudi Arabia), The Francis Crick Institute (United Kingdom), Imperial College (United Kingdom) and the Institute of Bioengeneering (Russia). The authors have published datasets related to the work, which can be reanalyzed by the community and are available in the GEO database (https://www.ncbi.nlm.nih.gov/geo/) using the access number GSE132192.

RIKEN

Related Dna Articles:

Zigzag DNA
How the cell organizes DNA into tightly packed chromosomes. Nature publication by Delft University of Technology and EMBL Heidelberg.
Scientists now know what DNA's chaperone looks like
Researchers have discovered the structure of the FACT protein -- a mysterious protein central to the functioning of DNA.
DNA is like everything else: it's not what you have, but how you use it
A new paradigm for reading out genetic information in DNA is described by Dr.
A new spin on DNA
For decades, researchers have chased ways to study biological machines.
From face to DNA: New method aims to improve match between DNA sample and face database
Predicting what someone's face looks like based on a DNA sample remains a hard nut to crack for science.
Self-healing DNA nanostructures
DNA assembled into nanostructures such as tubes and origami-inspired shapes could someday find applications ranging from DNA computers to nanomedicine.
DNA design that anyone can do
Researchers at MIT and Arizona State University have designed a computer program that allows users to translate any free-form drawing into a two-dimensional, nanoscale structure made of DNA.
DNA find
A Queensland University of Technology-led collaboration with University of Adelaide reveals that Australia's pint-sized banded hare-wallaby is the closest living relative of the giant short-faced kangaroos which roamed the continent for millions of years, but died out about 40,000 years ago.
DNA structure impacts rate and accuracy of DNA synthesis
DNA sequences with the potential to form unusual conformations, which are frequently associated with cancer and neurological diseases, can in fact slow down or speed up the DNA synthesis process and cause more or fewer sequencing errors.
Changes in mitochondrial DNA control how nuclear DNA mutations are expressed in cardiomyopathy
Differences in the DNA within the mitochondria, the energy-producing structures within cells, can determine the severity and progression of heart disease caused by a nuclear DNA mutation.
More DNA News and DNA Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Listen Again: The Biology Of Sex
Original broadcast date: May 8, 2020. Many of us were taught biological sex is a question of female or male, XX or XY ... but it's far more complicated. This hour, TED speakers explore what determines our sex. Guests on the show include artist Emily Quinn, journalist Molly Webster, neuroscientist Lisa Mosconi, and structural biologist Karissa Sanbonmatsu.
Now Playing: Science for the People

#569 Facing Fear
What do you fear? I mean really fear? Well, ok, maybe right now that's tough. We're living in a new age and definition of fear. But what do we do about it? Eva Holland has faced her fears, including trauma and phobia. She lived to tell the tale and write a book: "Nerve: Adventures in the Science of Fear".
Now Playing: Radiolab

The Wubi Effect
When we think of China today, we think of a technological superpower. From Huweai and 5G to TikTok and viral social media, China is stride for stride with the United States in the world of computing. However, China's technological renaissance almost didn't happen. And for one very basic reason: The Chinese language, with its 70,000 plus characters, couldn't fit on a keyboard.  Today, we tell the story of Professor Wang Yongmin, a hard headed computer programmer who solved this puzzle and laid the foundation for the China we know today. This episode was reported and produced by Simon Adler with reporting assistance from Yang Yang. Special thanks to Martin Howard. You can view his renowned collection of typewriters at: antiquetypewriters.com Support Radiolab today at Radiolab.org/donate.