Emerging concepts of lncRNA function Flashcards
What is lncRNA?
Long non-coding RNA
What is pervasive transcription? (2)
- Transcription outside of protein coding areas of the genome
- ENCODE project found ~75% of the human genome is transcribed producing lots of non-coding RNAs
What are examples of non-coding RNAs (ncRNAs)? (6)
- siRNA (small-interfering)
- rRNA (ribosomal)
- snoRNA (small nucleolar)
- miRNA (micro)
- tRNA (transfer)
- CUTs (cryptic upstream transcripts
How are lncRNAs defined? (5)
- Hard to classify
- Long RNA transcripts that DO NOT encode proteins
- Longer than 200nt
- Typically lack ORFs > 100 codons
- Typically don’t display conserved codon usage
What processes are lncRNAs involved in? (7)
- mRNA stability
- mRNA translation
- mRNA sponge
- Histone modification
- Transcriptional regulation
- Splicing
- Chromatin interactions
What are example classifications of lncRNA? (4)
- PROMPT
- Gene body associated RNA (antisense/sense)
- lincRNA
(- eRNA)
What is a PROMPT? (3)
- Promoter upstream transcript
- Bidirectional transcription from start sites generates antisense promoter transcripts
- Roles include promoting looping between enhancers and promoters
What are gene body associated RNAs?
Produced from transcription initiation in introns in an antisense direction, can also be sense
What is lincRNA? (2)
- Long intergenic non-coding RNA
- Transcribed from non-coding regions between genes
What is eRNA? (2)
- Enhancer RNA
- Transcribed from enhancer regions and regulate gene expression
What are examples of lincRNAs? (2)
- MALAT-1 (Neat2)
- Neat1
What is the function of MALAT-1 (Neat2)?
Involved in alternative splicing and nuclear organisation
What is the function of Neat1?
Involved in paraspeckle formation
What are examples of lncRNAs? (3)
- Xist
- MALAT-1
- Neat1
What is the function of Xist?
X chromosome inactivation
What is a drawback of RNAseq? (2)
- RNAseq is based on polyA selection or oligo d(T) priming for cDNA production and sequencing
- Fails to detect unprocessed lncRNA transcripts
What is a better way of measuring transcription levels in a cell?
Mapping locations of transcribing RNA polymerases instead of RNAseq
What are examples of methods of nascent RNA transcription mapping? (4)
- GROseq
- PROseq
- NETseq
- TTseq
What is GROseq? (2)
- Global run on sequencing
- Bromouridine incorporated into RNA in vivo and used to purify newly synthesised RNAs
What is PROseq? (2)
- Precision nuclear run on sequencing
- Development of GRO-seq with all bromo-dNTPs which improves base-pair resolution
What is NETseq? (2)
- Negative elongating transcript sequencing
- Immunoprecipitate transcribing RNA polymerases, brings the RNA with it
What is TTseq? (2)
- Transient transcriptome sequencing
- Nascent RNA labelled with 4-thiouridine and purified
What is nascent RNA?
RNA that is being actively transcribed by so is still associated with RNA polymerase II
What do you see in nascent RNA sequencing that you don’t get from normal RNA seq?
Shows you transcription in all areas of the genome not just protein-coding/polyA enriched areas