molecular biology Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and phys ...

, and more importantly high-throughput DNA sequencing, a chimera is a single DNA sequence originating when multiple transcripts or DNA sequences get joined. It can occur in various contexts. Chimeric reads are generally considered artifacts in sequencing applications (such a
amplicon sequencing
and are filtered out from the data during processing to prevent spurious inferences of biological variation. In a different context, the deliberate creation of artificial chimeras can also be a useful tool in the molecular biology. For example, in

protein engineering Protein engineering is the process of developing useful or valuable proteins. It is a young discipline, with much research taking place into the understanding of protein folding and recognition for protein design principles. It has been used to im ...

, "chimeragenesis (forming chimeras between proteins that are encoded by homologous cDNAs)" p. 424 is one of the "two major techniques used to manipulate cDNA sequences". For gene fusions that occur through natural processes, see chimeric genes and

fusion genes A fusion gene is a hybrid gene formed from two previously independent genes. It can occur as a result of translocation, interstitial deletion, or chromosomal inversion. Fusion genes have been found to be prevalent in all main types of human neopla ...

Description

Transcript chimera

A chimera can occur as a single cDNA sequence originating from two transcripts. It is usually considered to be a contaminant in transcript and

expressed sequence tag In genetics, an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence. ESTs may be used to identify gene transcripts, and were instrumental in gene discovery and in gene-sequence determination. The identification of ESTs has proc ...

(which results in the moniker of EST chimera) databases. It is estimated that approximately 1% of all transcripts in the

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. T ...

's Unigene database contain a "chimeric sequence".

PCR chimera

A chimera can also be an artifact of

PCR PCR or pcr may refer to: Science * Phosphocreatine, a phosphorylated creatine molecule * Principal component regression, a statistical technique Medicine * Polymerase chain reaction ** COVID-19 testing, often performed using the polymerase chain r ...

amplification. It occurs when the extension of an

amplicon In molecular biology, an amplicon is a piece of DNA or RNA that is the source and/or product of amplification or replication events. It can be formed artificially, using various methods including polymerase chain reactions (PCR) or ligase chain ...

is aborted, and the aborted product functions as a primer in the next PCR cycle. The aborted product anneals to the wrong template and continues to extend, thereby synthesizing a single sequence sourced from two different templates. PCR chimeras are an important issue to take into account during metabarcoding, where DNA sequences from environmental samples are used to determine biodiversity. A chimera is a novel sequence that will most probably not match to any known organism. Hence, it might be interpreted as a new species thereby overinflating the diversity.

Chimeric read

A chimeric read is a digital DNA sequence (i.e. a string of letters in a file that can be read as a DNA sequence) that originates from an actual chimera (i.e. a physical DNA sequence in a sample) ''or'' produced due to misreading the sample. The latter is known to occur with sequencing of

electrophoresis Electrophoresis, from Ancient Greek ἤλεκτρον (ḗlektron, "amber") and φόρησις (phórēsis, "the act of bearing"), is the motion of dispersed particles relative to a fluid under the influence of a spatially uniform electric f ...

gels. Chimeric reads are common with amplicon sequencing applications such as

16S rRNA gene 16S or 16s may refer to: * Ribosomal RNAs, in biology: ** prokaryotic 16S ribosomal RNA ** mitochondrial 16S ribosomal RNA * Myrtle Creek Municipal Airport's FAA identifier * Fujitsu Micro 16s, a 1983 Business personal computer *Sulfur Sulfu ...

sequencing, since closely related sequences are amplified. The most common mechanism is that incomplete extension during the PCR results in partial sequence strands that can act as primers in subsequent PCR cycles on similar but non identical sequences. Extension of such hybrid priming events causes the formation of chimeric sequences. Some computational methods have been devised to detect and remove chimeras, like: * CHECK_CHIMERA of the Ribosomal Database Project * ChimeraSlayer in QIIME * uchime in usearch * removeBimeraDenovo() in dada2 * Bellerophon * CATCh * DECIPHER

Examples

* "The first mRNA transcript isolated for..." the human gene C2orf3 "...was part of an artificial chimera..." * CYP2C17 was thought to be a human gene, but "...is now considered an artefact based on a chimera of CYP2C18 and CYP2C19." * Researchers have created receptor chimeras in their studies of Oncostatin M.

References