LncRNA GO annotation manual

LncRNAs have multiple and varied activities (see [PMID:31048766] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed here.

Decision tree to assist with curation of lncRNA:miRNA interactions

These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.

Link to LncRNA_Decision_Tree pdf[[1]]

Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs. The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.

Note: to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using has_input) if the evidence for binding is in another paper.

Inactivation of X chromosome by heterochromatin formation

Figure 2b [PMID:31048766]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.

LncRNA (Xist) Annotations:

• MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)
• BF: GO:0060820 inactivation of X chromosome by heterochromatin formation

DNA-DNA tethering activity

Figure 2c [PMID:31048766]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.

LncRNA (Firre) annotations:

• MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)
• BP: GO:0006325 chromatin organization

Promoter-enhancer loop anchoring activity

Figure 2d [PMID:31048766]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.

LncRNA (CCAT1-L) annotations:

• MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)
• BP: GO:0140588 chromatin looping

Regulation of chromatin accessibility

Figure 2e [PMID:31048766]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.

LncRNA (Xist) annotations:

• MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)
• BP: GO:0006338 chromatin remodeling

LncRNA (Mhrt) annotations based on [PMID:25119045]:

• MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)
• BP: GO:0006338 chromatin remodeling

Triplex-Mediated Changes in Chromatin Structure

Figure 2f, [PMID:31048766]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.

LncRNA (Khps1) annotations based on [PMID: 26590717]:

• MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)
• MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)
• BP: GO:0006325 chromatin organization
• BP: GO:0045944 positive regulation of transcription by RNA polymerase II

RNA polymerase inhibitor activity

Figure 2g, [PMID:31048766]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.

LncRNA annotations:

• MF: GO:0140870 RNA polymerase inhibitor activity
• BP:GO:0000122 negative regulation of transcription by RNA polymerase II

repressor of RNA polymerase inhibitor activity

Figure 2h, [PMID:31048766]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.

LncRNA (SLERT) annotations:

• MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)
• BP: GO:0045943 positive regulation of transcription by RNA polymerase I

molecular condensate scaffold activity

Figure 2i, [PMID:31048766]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.

LncRNA (NEAT1) annotations:

• MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)
• BP: GO:0030575 nuclear body organization

miRNA inhibitor activity / sponge

See decision tree above Figure 2k, [PMID:31048766]: A regulatory network consisting of different types of ncRNAs. Cyrano, harbouring miR-7 binding sites, targets miR-7 for degradation and prevents miR-7 from repressing its target RNAs including the circRNA Cdr1as.

LncRNA (Cyrano) annotations:

• MF GO:0140869 miRNA inhibitor activity via base-pairing + additional information (eg has_input miR-7 RNAcentral ID, part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)
• BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing

mRNA degradation

Figure 2l, [PMID:31048766]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.

LncRNA (NORAD) annotations:

• MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)
• BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing

mRNA translation repression

Figure 2m, [PMID:31048766]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.

LncRNA annotations:

• MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)
• BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing

regulation of post-translational modifications

Figure 2n, [PMID:31048766]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1.

LncRNA annotations:

• MF: GO:0019212 phosphatase inhibitor activity and/or GO:0140311 protein sequestering activity
• BP: may be able to associated a GO terms describing the regulation of signaling pathway or other process