Lnc-EPB41-Protein Interactions Associated with Congenital Pouch Colon

Gupta, Sonal; Gupta, Nidhi; Tiwari, Prabhat; Menon, Saji; Mathur, Praveen; Kothari, S. L.; Nallapeta, Sivaramaiah; Medicherla, Krishna Mohan; Suravajhala, Prashanth

doi:10.3390/biom8030095

Cited by 9 publications

(5 citation statements)

References 25 publications

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“…3). We observed several missense as well as frameshift variants to be in concordance with colorectal cancer exome datasets [38] besides a few non-coding RNAs especially lnc-EPB41-1-1 shown to be promiscuously interacting with KIF13A, a gene causal to CPC [39]. Furthermore, our microarray findings also show that few noncoding RNAs are differentially expressed in CPC samples [40].…”

Section: Congenital Pouch Colonsupporting

confidence: 76%

Is Pouch Specific to Colon and Not Ileum?

Gupta

Tiwari

Gupta³

et al. 2019

CPR

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Background: Congenital Pouch Colon (CPC) is an anorectal anomaly with an incidence of 3.5:1 in males and females, respectively. We have earlier reported CPC to be quite prevalent in north Indian tertiary care centers. Objective: n this article, we deliberate on the possible causes associated with CPC bringing the manifestation of the disease. In addition, we throw insights on the effective role of this congenital anomaly in Colon and provide systems genomic evaluation by comparing our recent analysis to that of Colon and Ileum based on Next-Generation Sequencing (NGS) studies. Conclusions: In this commentary article, we argue that a host of epigenetic factors could be the reason why the disease is manifested in colon alone. We further hypothesize on the few unmet challenges linking epigenetics to understand the genetic variants.

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Section: Congenital Pouch Colonsupporting

confidence: 76%

Is Pouch Specific to Colon and Not Ileum?

Gupta

Tiwari

Gupta³

et al. 2019

CPR

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“…There are different computational approaches for the identification of lncRNAs from the genome as well as transcriptome data, investigation of lncRNA functions, and its associated regulatory networks. Although identifying lncRNAs is out of the question from whole exome sequencing, recent reports including ours have shown how the third generation sequencing technology is used to screen the lncRNAs from exomes [ 46 , 47 ]. Nevertheless, the lncRNAs are ascertained as differentially expressed gene (DEG) counts and many of them turn out to be up/downregulated.…”

Section: Identification and Functional Characterization Of Lncrnasmentioning

confidence: 99%

Long Non-Coding RNAs in Insects

Choudhary

Sharma

Meghwanshi

et al. 2021

Animals

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Only a small subset of all the transcribed RNAs are used as a template for protein translation, whereas RNA molecules that are not translated play a very important role as regulatory non-coding RNAs (ncRNAs). Besides traditionally known RNAs (ribosomal and transfer RNAs), ncRNAs also include small non-coding RNAs (sncRNAs) and long non-coding RNAs (lncRNAs). The lncRNAs, which were initially thought to be junk, have gained a great deal attention because of their regulatory roles in diverse biological processes in animals and plants. Insects are the most abundant and diverse group of animals on this planet. Recent studies have demonstrated the role of lncRNAs in almost all aspects of insect development, reproduction, and genetic plasticity. In this review, we describe the function and molecular mechanisms of the mode of action of different insect lncRNAs discovered up to date.

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“…Briefly, WES was performed on an Illumina multiplexed sequencer with paired-end chemistry and 110x effective coverage. Using our in-house developed pipeline [19], all unmapped sequence reads were aligned to the human reference genome (hg38) and variants were called. The mutations from WES study were checked to discover the variants, if any, across the samples (Figure 2).…”

Section: Variant Annotation Filtering and Quality Controlmentioning

confidence: 99%

Whole Exome-Trio Analysis Reveals Rare Variants Associated with Congenital Pouch Colon

Gupta

Mathur

Mishra³

et al. 2023

Children

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Anorectal malformations (ARM) are individually common, but Congenital Pouch Colon (CPC) is a rare anorectal anomaly that causes a dilated pouch and communication with the genitourinary tract. In this work, we attempted to identify de novo heterozygous missense variants, and further discovered variants of unknown significance (VUS) which could provide insights into CPC manifestation. From whole exome sequencing (WES) performed earlier, the trio exomes were analyzed from those who were admitted to J.K. Lon Hospital, SMS Medical College, Jaipur, India, between 2011 and 2017. The proband exomes were compared with the unaffected sibling/family members, and we sought to ask whether any variants of significant interest were associated with the CPC manifestation. The WES data from a total of 64 samples including 16 affected neonates (11 male and 5 female) with their parents and unaffected siblings were used for the study. We examined the role of rare allelic variation associated with CPC in a 16 proband/parent trio family, comparing the mutations to those of their unaffected parents/siblings. We also performed RNA-Seq as a pilot to find whether or not the genes harboring these mutations were differentially expressed. Our study revealed extremely rare variants, viz., TAF1B, MUC5B and FRG1, which were further validated for disease-causing mutations associated with CPC, further closing the gaps of surgery by bringing intervention in therapies.

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Lnc-EPB41-Protein Interactions Associated with Congenital Pouch Colon

Cited by 9 publications

References 25 publications

Is Pouch Specific to Colon and Not Ileum?

Is Pouch Specific to Colon and Not Ileum?

Long Non-Coding RNAs in Insects

Whole Exome-Trio Analysis Reveals Rare Variants Associated with Congenital Pouch Colon

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