Difference between revisions of "Transcriptomics"
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| − | <h1> | + | <h1><font size="3">Definition</font></h1> |
| − | < | + | <p><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">The </span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">transcriptome</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> is the set of all RNA molecules, including </span><a href="http://en.wikipedia.org/wiki/Messenger_RNA" title="Messenger RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">mRNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, </span><a href="http://en.wikipedia.org/wiki/Ribosomal_RNA" title="Ribosomal RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">rRNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, </span><a href="http://en.wikipedia.org/wiki/Transfer_RNA" title="Transfer RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">tRNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, and other </span><a href="http://en.wikipedia.org/wiki/Non-coding_RNA" title="Non-coding RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">non-coding RNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> </span><a href="http://en.wikipedia.org/wiki/Transcription_(genetics)" title="Transcription (genetics)" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">transcribed</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> in one cell or a population of </span><a href="http://en.wikipedia.org/wiki/Cell_(biology)" title="Cell (biology)" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">cells</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">. </span></p> |
| − | < | + | <h1><font size="3">mRNA</font></h1> |
| − | < | + | <p><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">Messenger RNA</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> (</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">mRNA</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">) is a large family of </span><a href="http://en.wikipedia.org/wiki/RNA" title="RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> molecules that convey </span><a href="http://en.wikipedia.org/wiki/Genetic_information" title="Genetic information" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">genetic information</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> from </span><a href="http://en.wikipedia.org/wiki/DNA" title="DNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">DNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> to the </span><a href="http://en.wikipedia.org/wiki/Ribosome" title="Ribosome" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">ribosome</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, where they specify the </span><a href="http://en.wikipedia.org/wiki/Amino_acid" title="Amino acid" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">amino acid</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">sequence of the </span><a href="http://en.wikipedia.org/wiki/Protein" title="Protein" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">protein</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> products of </span><a href="http://en.wikipedia.org/wiki/Gene_expression" title="Gene expression" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">gene expression</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">. Following </span><a href="http://en.wikipedia.org/wiki/Transcription_(genetics)" title="Transcription (genetics)" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">transcription</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> of </span><a href="http://en.wikipedia.org/wiki/Primary_transcript" title="Primary transcript" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">primary transcript</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> mRNA (known as </span><a href="http://en.wikipedia.org/wiki/Precursor_mRNA" title="Precursor mRNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">pre-mRNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">) by </span><a href="http://en.wikipedia.org/wiki/RNA_polymerase" title="RNA polymerase" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA polymerase</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, processed, mature mRNA is </span><a href="http://en.wikipedia.org/wiki/Translation_(genetics)" title="Translation (genetics)" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">translated</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> into a polymer of amino acids</span></p> |
| − | < | + | <h1><span style="font-size: medium;">UTR</span></h1> |
| − | < | + | <p><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">In </span><a href="http://en.wikipedia.org/wiki/Molecular_genetics" title="Molecular genetics" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">molecular genetics</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, an </span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">untranslated region</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> (or </span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">UTR</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">) refers to either of two sections, one on each side of a </span><a href="http://en.wikipedia.org/wiki/Coding_sequence" title="Coding sequence" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">coding sequence</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> on a strand of </span><a href="http://en.wikipedia.org/wiki/MRNA" title="MRNA" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">mRNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">. If it is found on the 5' side, it is called the </span><a href="http://en.wikipedia.org/wiki/Five_prime_untranslated_region" title="Five prime untranslated region" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">5' UTR</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> (or </span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">leader sequence</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">), or if it is found on the 3' side, it is called the </span><a href="http://en.wikipedia.org/wiki/Three_prime_untranslated_region" title="Three prime untranslated region" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">3' UTR</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> (or </span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">trailer sequence</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">).</span></p> |
| − | < | + | <h1><span style="font-size: medium;">ncRNA</span></h1> |
| − | < | + | <p><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">A </span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">non-coding RNA</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> (</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">ncRNA</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">) is a functional </span><a href="http://en.wikipedia.org/wiki/RNA" title="RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> molecule that is not </span><a href="http://en.wikipedia.org/wiki/Translation_(genetics)" title="Translation (genetics)" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">translated</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> into a </span><a href="http://en.wikipedia.org/wiki/Protein" title="Protein" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">protein</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">. </span><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">Non-coding RNA genes include highly abundant and functionally important RNAs such as </span><a href="http://en.wikipedia.org/wiki/Transfer_RNA" title="Transfer RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">transfer RNAs</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> (tRNAs) and </span><a href="http://en.wikipedia.org/wiki/Ribosomal_RNA" title="Ribosomal RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">ribosomal RNAs</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">(rRNAs), as well as RNAs such as </span><a href="http://en.wikipedia.org/wiki/MicroRNA" title="MicroRNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">microRNAs</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, </span><a href="http://en.wikipedia.org/wiki/SiRNA" title="SiRNA" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">siRNAs</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, and </span><a href="http://en.wikipedia.org/wiki/SnRNA" title="SnRNA" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">snRNAs</a>.</p> |
| − | < | + | <h1><span style="font-size: medium;">poly A</span></h1> |
| + | <p><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">Polyadenylation</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> is the addition of a </span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">poly(A) tail</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> to a </span><a href="http://en.wikipedia.org/wiki/Messenger" title="Messenger" class="mw-disambig" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">messenger</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> </span><a href="http://en.wikipedia.org/wiki/RNA" title="RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">. </span><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">The poly(A) tail is important for the nuclear export, translation, and stability of mRNA. The tail is shortened over time, and, when it is short enough, the mRNA is enzymatically degraded.</span></p> | ||
| + | <h1><span style="font-size: medium;">measurment of RNA expression</span></h1> | ||
| + | <p><a href="http://en.wikipedia.org/wiki/RNA-seq" title="RNA-seq" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA-seq</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> is emerging (2013) as the method of choice for measuring transcriptomes of organisms, though the older technique of </span><a href="http://en.wikipedia.org/wiki/DNA_microarray" title="DNA microarray" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">DNA microarrays</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"> is still used.</span></p> | ||
| + | <h1> </h1> | ||
| + | <h1><span style="font-size: medium;">Relationship between genomics and transcriptomics</span></h1> | ||
| + | <h1><span style="font-size: medium;">Relationship between Transcriptome and Proteome</span></h1> | ||
| + | <h1> </h1> | ||
| + | <h1> </h1> | ||
Revision as of 14:04, 22 May 2015
Contents
Definition
The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA transcribed in one cell or a population of cells.
mRNA
Messenger RNA (mRNA) is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acidsequence of the protein products of gene expression. Following transcription of primary transcript mRNA (known as pre-mRNA) by RNA polymerase, processed, mature mRNA is translated into a polymer of amino acids
UTR
In molecular genetics, an untranslated region (or UTR) refers to either of two sections, one on each side of a coding sequence on a strand of mRNA. If it is found on the 5' side, it is called the 5' UTR (or leader sequence), or if it is found on the 3' side, it is called the 3' UTR (or trailer sequence).
ncRNA
A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. Non-coding RNA genes include highly abundant and functionally important RNAs such as transfer RNAs (tRNAs) and ribosomal RNAs(rRNAs), as well as RNAs such as microRNAs, siRNAs, and snRNAs.
poly A
Polyadenylation is the addition of a poly(A) tail to a messenger RNA. The poly(A) tail is important for the nuclear export, translation, and stability of mRNA. The tail is shortened over time, and, when it is short enough, the mRNA is enzymatically degraded.
measurment of RNA expression
RNA-seq is emerging (2013) as the method of choice for measuring transcriptomes of organisms, though the older technique of DNA microarrays is still used.
