ten. On the whole, I usually do not find the Supplementary Files especially helpful or related towards the paper. Authors response, The Supplementary Files are modified during the revised manuscript. We have only integrated Tables and Figures appropriate to your paper and removed the redundant ones. I thank the Authors for responding comprehensively to my comments. I continue to have doubts in regards to the worth of this paper. I’ve the impression that the ana lysis and manuscript preparation has been carried within a rather careless way, without consideration from the impli cations in the perform, or for with clarity for the reader. Moreover, I’m concerned through the lack of clarity in the Authors about no matter whether the claimed smaller RNA more than laps are taking place around the very same strand as the claimed host lncRNA a problem of crucial significance to this manuscript.
Authors response, We have analyzed the smallRNA clusters as annotated by DeepBase and falling RGFP109 while in the exact same orientation because the lncRNA. The manuscript segment is modified appropriately to detail the evaluation methodology. We agree with all the reviewer the com putational analysis will not give considerably insight to the possible biological implications of the observation. In truth, in existing circumstance, our comprehending of bio logical functions for bulk of lncRNAs is not regarded and computational strategies to functionally assign roles are nonetheless na ve. The current report serves as being a beginning point and ready reference to a dataset which suggests that a subset of lncRNAs could possibly be processed to smaller sized RNAs.
Within the revised manuscript, selleckchem we detail our observation on a reasonably nicely studied lncRNA. The lncRNA PTENTP1 is actually a pseudogene of PTEN gene. Our analysis reveals that PTENP1 harbors five little RNAs clusters as annotated by deepBase. This observation can be corroborated by inde pendent dataset of smaller RNA cloning data from smiRNAdb which revealed the fifth cluster com prises of three distinct little RNA clusters, obtaining vary ential expression ranges in different tissues as depicted in Figure1. This could lead to a likelihood whereby other than the PTENP1 function, the processed modest RNAs can be an extra mechanism for modulating bio logical processes in the cell and possibly while in the patho genesis of oncogenesis. We’ve got compiled our leads to tabular format that is offered as well as manuscript as supplemental files, the place we have now outlined that compact RNAs are mapped onto the sense strand of lncRNAs.
While the topic of lncRNA processing into tiny RNAs is surely an exciting and timely one, the current manuscript does little to handle to me the fundamental inquiries from the field, Are lncRNAs processed to little RNAs Do these arise preferentially from exons or introns Does this course of action come about at a charge that exceeds background possibility Do these smaller RNAs display any evi dence for function Do these tiny RNAs have interesting and realistic tissue ex pression profiles Are these little RNAs marked by any type of epigenetic signal and so on.