euGenes/Arthropods About Arthropods EvidentialGene DroSpeGe

Conserved Arthropod long noncoding (lncrna) adjacent to protein coding genes, or UTR extensions

Expanded document on
Conserved long non-coding RNA expression and genes in wasp, bee, ant, fly and mouse, 2016.05, part of Nasonia wasp genes doc doi:10.1186/s12864-016-2886-9


Notes:
  • protein + lncrna genes shown are all conserved with DrosMel lncrna/utr3 (ref:doi:10.1016/j.celrep.2012.01.001)
  • lncrna spans are often expressed at levels above protein coding exons
  • lncrna spans may be longer than protein coding transcript, some by 10k's
  • some Daphnia cases show bi-directional expression in lncrna spans. This is consistent with literature reports of antisense and bi-directional lncrna associated with protein coding genes.
  • Daphnia intergenic spans are compressed versus insects, and as oberved here, lncrna spans often extend with strong expression completely between coding exons of two genes (often reversed). This can lead to problem transcript assemblies composed of many genes and lncrna in between.
  • at least some of these are also found in other insect de-novo transcript assemblies as long utrs (ELAV/fne case for whitefly was "problem" assembly leading to this list).
Don Gilbert, 2013 January, part of EvidentialGene transcript assembly improvement effort.

Example gene maps

gene: RNA-Binding protein, fne (Found in NEurons) or ELAV-like FlyBase:FBgn0086675, RefSeq:NP_572842
Daphnia
genomap2013-01-30-11.46.55
Aphid
genomap2013-01-30-11.42.07
Wasp
genomap2013-01-30-11.36.51
gene: Calmodulin, FlyBase:FBgn0000253,RefSeq:NP_523710.1
Daphnia
genomap2013-01-29-4.44.31
Aphid
genomap2013-01-29-4.44.50
Wasp
genomap2013-01-29-4.43.46
gene: casein kinase II , FlyBase:FBgn0000259, RefSeq:NP_996415.1
Daphnia
genomap2013-01-29-4.42.59
Aphid
genomap2013-01-29-4.42.50
Wasp
genomap2013-01-29-4.43.15
gene: odd-skipped/gonadotropin inducible transcription factor, FlyBase:FBgn0000286, RefSeq:NP_523474.1
Daphnia
genomap2013-01-29-4.40.33
Aphid
genomap2013-01-29-4.39.25
Wasp
genomap2013-01-29-4.40.51
gene: Tyrosine-protein phosphotase
Daphnia
genomap2013-01-29-4.38.17
Aphid
genomap2013-01-29-4.38.25
Wasp
genomap2013-01-29-4.38.07
gene: cAMP-specific 3',5'-cyclic phosphodiesterase/dunce, FlyBase:FBgn0000479, RefSeq:NP_726849.1
Daphnia
genomap2013-01-29-4.34.43
Aphid
genomap2013-01-29-4.33.35
Wasp
genomap2013-01-29-4.34.11
gene: homeobox protein extradenticle, FlyBase:FBgn0000611, RefSeq:NP_523360.1
Daphnia
genomap2013-01-29-4.32.34
Aphid
genomap2013-01-29-4.33.09
Wasp
genomap2013-01-29-4.32.55


References

Ponjavic J, Oliver PL, Lunter G, Ponting CP (2009) Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain. PLoS Genet 5(8): e1000617. doi:10.1371/journal.pgen.1000617
.. brain-expressed long ncRNAs are preferentially located adjacent to protein-coding genes that are (1) also expressed in the brain and (2) involved in transcriptional regulation or in nervous system development

Young.., Ponting CP (2012) Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome Genome Biol. Evol. 4(4):427–442 doi:10.1093/gbe/evs020
.. involved in the regulation of neighboring protein-coding genes

Global Patterns of Tissue-Specific Alternative Polyadenylation in< i> Drosophila P Smibert, P Miura, JO Westholm, S Shenker, G May… - Cell reports, 2012 doi:10.1016/j.celrep.2012.01.001
"Genes encoding RNA binding proteins (RBPs) and transcription factors were preferentially subject to 30 UTR extensions; .. longest in c. nervous tissue .. Many of these exceeded the longest RNA size standards, including the existence of full-length mei-P26 transcripts estimated from RNA-seq data to be some 23 kb in length, of which >18 kb was UTR.

Dicer + lncrna: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859052/
Examples of potential functional conserved lncRNAs include cases that overlap Dicer and U2AF2. Dicer is an endoribonuclease that cleaves double-stranded RNAs into shorter double-stranded segments called small interfering RNAs (siRNAs)

Cow lncrla: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412814/
23,060 bovine ncRNAs: Many of these intergenic non-coding RNAs mapped close to the 3' or 5' end of thousands of genes and many of these were transcribed from the opposite strand with respect to the closest gene, particularly regulatory-related genes


Developed at the Genome Informatics Lab of Indiana University Biology Department