Page 47 - Biennial Report 2018-20 Jun 2021

STRUCTURE-FUNCTION DYNAMICS OF lncRNA CONCR AND THE HELICASE

DDX11 IN REGULATING SISTER CHROMATID COHESION

In the area of functional genomics, a pivotal discovery of recent times is that the vast majority
of RNA molecules in the mammalian cell are non-coding, i.e. they do not give rise to proteins.
They can fold upon themselves, form structures that rival proteins in their complexity and
engage in charge and shape-based interactions forming catalytic domains or structural scaffolds
of large ribonucleoprotein complexes. They can also use classical hybridization to bind to DNA
or other RNA molecules, forming bridges between DNA and protein.
Mary Ekka has initiated a DST funded project examining the role of the lncRNA CONCR (cohesion
regulator noncoding RNA) in abolishing birth defects caused due to faulty sister chromatid
cohesion. The lncRNA CONCR (cohesion regulator noncoding RNA) is found to be essential for
sister chromatid cohesion establishment during cell division. CONCR was upregulated in multiple
cancer types and is closely associated with p53. Deletion of p53 causes an upregulation in CONCR
expression. CONCR was found to be necessary for proper DNA replication and its depletion leads
to severe sister chromatid cohesion defects. CONCR is transcribed in antisense from the DDX11
promoter. DDX11 is a superfamily 2 DNA helicase involved in proper chromosome cohesion at
both the centromeres and along the chromosome arms, as well as tight binding of cohesion
complexes to chromatin. Loss of this protein leads to embryonic lethality. An earlier report had
suggested that CONCR binds to DDX11
and the defects caused due to sister
chromatid cohesion loss upon CONCR
depletion can be rescued by
overexpression of DDX11, thus proving
that both protein and RNA function in a
common pathway. The broad objectives
of this project include the identification
of small conserved motifs in CONCR that
can modulate its function. The genomic
locus of CONCR was identified and its
sequence retrieved using an informatics
approach. Further, its expression was
validated in different cell lines using qRT
PCR.

Another objective is the examination
and characterization of CONCR and
DDX11 interaction along with
investigating its energetics and kinetics.
Through different biophysical
approaches, modulation of the activity
of DDX11 upon interaction can be
studied. Using a combination of deletional, mutational studies as well as biophysical approaches,
secondary structures in CONCR and conserved RNA motifs that can mediate RNA-protein binding
can be studied also providing mechanistic insight into the formation and role of these structures.

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