lncRNA Conference Call Minutes – 2 nd August 2011

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lncRNA

Conference Call Minutes


2
nd

August

2011


Present:

Jen Harrow,
Mark Thomas, Gloria Despacio
-
Reyes, Rory Johnson,

Sarah ? (CRG), Balazs Banfai,
Charlie Steward, Baikang Pei, Tom Gingeras, Tejaswini Mishra,

Leonard Lipovich, Jeffrey Loeb
, Mark
Diekhans, Ben Brown
, Hui Ja
, Arif Harmanci


Notes from last minutes



No comments
/questions


Systems biology of human brain activity:

Computational
-
experimental integration

assigns lncRNAs
into regulatory networks

(LL/JL)



Introduction by
JL



Seizure

-

background



Remote symptomatic epilepsy proportional incidence by age and etiology



Systems Biology of Epilepsy Project (SBEP)



I
ntroduction



Interictal spiking is far more frequent than seizures



M
ap spiking to areas of brain

and study tissue samples using genomics, proteomics, metabolomics



Detail of collaborative work by LL



C
onstruction
and refinement of a human lncRNA

TU

catalog and custom microarray



6736 candidates



Coding
-
noncoding integration of

transcriptome data from t
he
in vivo

human epileptic brain



Integrated coding/noncoding transcriptomics of the human neocortex reveals 8 co
-
DE activity
-
dependent
lncRNA
-
mRNA cis
-
pairs and 349 additional lncRNAs



BDNF is a key regulator in epilepsy



Complexity of an lncRNA
-
encoding gen
omic landscape: The lncRNA gene BDNFOS shares the LIN7C
bidirectional promoter and is cis
-
antisense to BDNF



BDNFOS splice sites are poorly conserved: NEW regulation of the OLD gene BDNF by an antisense
RNA?



qPCR confirms co
-
differential expression of an mR
NA
-
lncRNA pair in human pediatric neocortical epilepsy
(1 patient = 1 spiking vs nonspiking sample pair)



The human SH
-
SY5Y neuroblastoma cell line, treated with repeated depolarization, recapitulates the
CREB activation and BDNFOS
-
BDNF co
-
expression observ
ed in epilepsy patients



RNAi of the lncRNA BDNFOS increases the mRNA levels of its cis
-
antisense partner BDNF, suggesting
that BDNFOS regulates BDNF



The human AK093366
-
AG2 lncRNA
-
mRNA cis
-
antisense pair: an Alu
-
harbored ncRNA splice site



Of 1,961 ncRNA gen
es in human cis
-
antisense pairs, 361 (18%), incl. AK093366
-
AG2, structurally depend
on primate
-
specific Alu repeats which harbor transcription starts, splice sites, and/or 3’ends



A known nuclear RNA
-
mediated RNA
-
maturation regulatory network induced in hum
an pediatric
neocortical epilepsy?



The Next Steps



Create a unified custom human lncRNA microarray, joining
the

CRG array lncRNAs with the Wayne
State
lncRNAs

2




Would ENCODE/
GENCODE members be potentially interested in work
i
ng with us on custom
-
array
and/or
RNAseq analysis of the
in vivo

human brain transcriptome, using our existing, and/or addit
ional
future, epilepsy samples?



Questions regarding how RNA can be extracted, technical replicates


GENCODE
7 lncRNA ORF mass spec update: genome
-
anchored and genome
-
independent approaches
to determining whether any lncRNAs are translated

(BB/
LL/
HJ)



GENCODE 7 lncRNA genes are 20
fold depleted for peptide hits

-

stronge
r effect than was observed for
3c



Mapping become cleaner (so slightly unfair comparison)



lncRNAs

are not enriched for weak peptide hits

(GM12878 nuclear fraction)



Accounting for expression, lncRNAs are ~4.5 fold depleted for peptides



Will add confidence bands later



Expression correlates with
(mass spec)
detectability differently across compartments (
GM12878)



Accounting for expression level differences we see that correlation is negative for lowly expressed genes



To do



biclustering analysis and/or machine learning



RJ Q
:

D
o
really short peptides
show up in mass spec
?, A: not sure, will chase up



Discussion regarding levels of expression and short RNAs


Method Slide (LL)



LL explained method used



Example: EMG1 locus



Antisense biotype may need to be reconsidered



LL to send list to Sanger


Update on H
avana incorporation of 4321 lncRNAs on GRCh3
7 from
Jai et al. (JH
)



Update on
lncRNA

data from LL overview



Filtered set



144 manually annotated



961 to look at



Examples



AX721191.1


sense_overlapping (Chr14)



CR620068.1


to be experimentally confirmed

(Chr14)



AK1249439


lincRNA (Chr15)



AK130626.1


retained
intron (Chr11)

o

LL can check microarray data

o

Discussion regarding poly A

o

Should import TG models (latest version)



AL109670.1


lincRNA (Chr15)



Add to agenda item for next call



Discussion regarding TG de novo models


For more detail regarding this call
please refer to the presentation
s

and/or WebEx recording available on the
GENCODE wiki


Next Teleconference will be held on

16
th

August

2011

at

4pm
BST (
GMT
+1)