TY - JOUR
T1 - Navigating the pitfalls of mapping DNA and RNA modifications
AU - Kong, Yimeng
AU - Mead, Edward A.
AU - Fang, Gang
N1 - Funding Information:
The work was funded by R01 HG011095 (G.F.) and R35 GM139655 (G.F.) from the National Institutes of Health (NIH).
Publisher Copyright:
© 2023, Springer Nature Limited.
PY - 2023
Y1 - 2023
N2 - Chemical modifications to nucleic acids occur across the kingdoms of life and carry important regulatory information. Reliable high-resolution mapping of these modifications is the foundation of functional and mechanistic studies, and recent methodological advances based on next-generation sequencing and long-read sequencing platforms are critical to achieving this aim. However, mapping technologies may have limitations that sometimes lead to inconsistent results. Some of these limitations are technical in nature and specific to certain types of technology. Here, however, we focus on common (yet not always widely recognized) pitfalls that are shared among frequently used mapping technologies and discuss strategies to help technology developers and users mitigate their effects. Although the emphasis is primarily on DNA modifications, RNA modifications are also discussed.
AB - Chemical modifications to nucleic acids occur across the kingdoms of life and carry important regulatory information. Reliable high-resolution mapping of these modifications is the foundation of functional and mechanistic studies, and recent methodological advances based on next-generation sequencing and long-read sequencing platforms are critical to achieving this aim. However, mapping technologies may have limitations that sometimes lead to inconsistent results. Some of these limitations are technical in nature and specific to certain types of technology. Here, however, we focus on common (yet not always widely recognized) pitfalls that are shared among frequently used mapping technologies and discuss strategies to help technology developers and users mitigate their effects. Although the emphasis is primarily on DNA modifications, RNA modifications are also discussed.
UR - http://www.scopus.com/inward/record.url?scp=85146386846&partnerID=8YFLogxK
U2 - 10.1038/s41576-022-00559-5
DO - 10.1038/s41576-022-00559-5
M3 - Review article
AN - SCOPUS:85146386846
SN - 1471-0056
JO - Nature Reviews Genetics
JF - Nature Reviews Genetics
ER -