amoldeep singh kainth

[amoldeep singh kainth @amoldeepkainth]

Does an RNA-binding protein need to recognize a specific RNA to be regulated by RNA?

Our new work shows promiscuous RNA binding by WDR5 can remodel and inhibit the MLL1/KMT2A histone methyltransferase complex.

https://t.co/9ZxIcr07oe
@MolecularCell

[Surabhi Chowdhary @surabhi_txn]

Our latest preprint on emergent #3Dgenome reorganization from the stepwise assembly of the #transcriptional #condensates. Check it out! #GeneExpression #chromatin @generegulation @Pha_Tran_Papers @4DNucleome #cellularstress https://t.co/d1ONJsvGJF

[amoldeep singh kainth @amoldeepkainth]

Plz 📖 for 1. Critical comparison of short & #longreadRNAseq 2. A read processing pipeline (SLURP) to orient #nanopore long reads 3. Impact of a longread artifact 4. A hybrid pipeline (TASSEL) to improve #transcriptomics. @gabihaddad08 https://t.co/FOX2uhBQvE #PLOSCompBio

[amoldeep singh kainth @amoldeepkainth]

@goekelab Hi, I am glad (and honored) that your group discussed our paper. As you mentioned, Bambu performed very well in our hands. I would really like to use it further but I have some questions regarding it. Will it be possible to connect over email?

[Surabhi Chowdhary @surabhi_txn]

Incredibly excited to share my academic experiences for the Young Researcher Series in TCB! Join me in celebrating diversity and expressing gratitude to Ilaria and the entire team of TCB @TrendsCellBio @i_carnevale
@UChicagoBSD @bsdpostdoc @DiversInclBSD
https://t.co/88LPbWU2gC

[amoldeep singh kainth @amoldeepkainth]

@CallumJCParr @gabihaddad08 This is an interesting idea. I will try it and update accordingly. Thanks.

[amoldeep singh kainth @amoldeepkainth]

Excited to share our work where we directly compare short & long-read RNAseq, discover a major artifact in long reads, design a pipeline to strand long reads & develop a hybrid method to improve transcript assembly. @gabihaddad08 @RNASeqBlog @nanopore https://t.co/01Bmw50S3m

[amoldeep singh kainth @amoldeepkainth]

@CallumJCParr @gabihaddad08 You are absolutely right. Direct RNA seems to be the way to go. As you said, it leads to better assembly without cDNA artifacts. Thanks again for your thoughtful discussion.

[amoldeep singh kainth @amoldeepkainth]

@CallumJCParr @gabihaddad08 Thanks for letting me know. The pages are public now.

[amoldeep singh kainth @amoldeepkainth]

@CallumJCParr @gabihaddad08 Our stranding method is only a small portion of the paper. We show that our merge of short and stranded long reads (regardless of how you strand reads) improves transcript assembly.

[amoldeep singh kainth @amoldeepkainth]

@CallumJCParr @gabihaddad08 The default pychopper was least effective as it also assembled transcripts on the wrong strand. (C) SLURP also led to assembly of complete transcripts in the correct direction (D) taking far less time to complete. I will be happy to take your further inputs over email.

[amoldeep singh kainth @amoldeepkainth]

@ThePhDPlace P=0.05

[Surabhi Chowdhary @surabhi_txn]

Thanks Alie for writing up such a beautiful piece on our recent study on #transcriptional #condensates drive #3Dgenome organization in the #heatshockresponse. @amoldeepkainth @UChicago @UChicagoBSD @lab_gross

[Surabhi Chowdhary @surabhi_txn]

Yay! we made it to the cover! We are very grateful to @MolecularCell for featuring our article on #transcriptional #condensates that drive #3Dgenome organization in the #heatshockresponse on their cover. Many thanks to @amoldeepkainth for conceptualizing and designing it!

[amoldeep singh kainth @amoldeepkainth]

Happy to contribute to this work @MolecularCell: Transcriptional condensates modulate 3D genome contacts. Their impact goes beyond transcription for cellular fitness. @Pha_Tran_Papers @ChromatinHaiku @generegulation @3D_Genome @4DNucleome

[Surabhi Chowdhary @surabhi_txn]

Beyond excited to share our article on #transcriptional #condensates that drive #3Dgenome organization in the #heatshockresponse. Were these HSR condensates primordial #superenhancers? @4Dnucleome @Pha_Tran_Papers @3D_Genome @BioCondensates
https://t.co/VHy1T1q3kH

[amoldeep singh kainth @amoldeepkainth]

@drkellyallen We need a big splash

[amoldeep singh kainth @amoldeepkainth]

@RVirologist I will wait for the paper “with bated breath”..

[Chicago RNA Club @rna_chicago]

Come join us March 9th at UChicago for our next RNA Club! Looking forward to talks by @amoldeepkainth, @DavidBushhouse, and Clayton Wollner

[amoldeep singh kainth @amoldeepkainth]

Is it the #enhancer element, act of #transcription or the #lncRNA itself that regulates a given gene? @JohnathonMHall et al developed omegazymes to answer these questions for a novel lncRNA in cardiac development.