Chapter 12: Transcriptomes

Question 1

a single gene can give rise to many mRNAs

• In this example, the gene has four exons, three alternative transcription startpoints, and three alternative transcription endpoints.
• If every combination of start- and endpoints is allowed and every possible combination of exons is used, then 135 different transcripts could be synthesized from this gene.
• This assumes that exons can be omitted from the mRNA but that the order of exons cannot be changed (for example, 1-3-4 is possible but not 1-4-3).
• This assumption is in accord with what we know about alternative splicing.

Answer 1

Five of the transcripts that could be obtained from the gene are shown.

Question 2

sncRNAs and lncRNAs

Answer 2

• sncRNAs: shorter than 200 nucleo tides are called short noncoding RNAs
• lncRNAs: longer ones, are called long noncoding RNAs

Question 3

Short noncoding RNAs

Short interfering RNAs (siRNAs)

Answer 3

• 20–25 nucleotides in length
• involved in the RNA interference pathway, which results in silencing of particular mRNAs
• Silencing occurs because an siRNA base­pairs to a region in the target mRNA, forming a double­stranded structure that is cut by a nuclease

Question 4

MicroRNAs (miRNAs)

Answer 4

• similar to siRNAs and also participate in RNA interference
• difference is that miRNAs are synthesized by cleavage of precursor molecules that form stem–loop structures, whereas the precursors of siRNAs are linear molecules

Question 5

Piwi-interacting RNAs (piRNAs)

Answer 5

• 25–30 nucleotides and hence slightly longer than siRNAs or miRNAs
• associate with piwi proteins
• their roles are not fully understood
• They participate in RNA interference but are also involved in other processes that result in repression of gene activity and, in particular, prevent expression of the genes present in retrotransposons by mRNA silencing and also by methylation of the DNA copies of these elements.

Question 6

Long noncoding RNAs, long intergenic noncoding RNAs (lincRNAs)

Answer 6

• long noncoding RNAs that collectively cover a large proportion of the intergenic space within a genome
• synthesized only in certain tissues or at certain developmental stages
• individual copy numbers are, much lower than mRNA copy numbers
• some map within the introns of mRNA transcription units
• others overlap with protein­coding exons
• assigning functions has proven difficult
• some functions are known: X inactivation process, genomic imprinting
• some ontain binding sites for transcription factors and act as decoys for regulatory proteins
  
  • result in down­regulation of transcription
  • ould be a genuine regulatory function,
• some believe they are junk that the cell is unable to get rid of
• a growing list of
  human diseases and developmental abnormalities that are associated with transcription of one of more of these RNAs