How to scan PROMOTERS to identify binding sites for TRANSCRIPTION FACTORS

Primer designing tutorial flanking a specific sequence
• Primer design for ChIP...
Primer designing tutorial using primer blast
• How to design primers ...
How to analyze the quality of a good primer
• How to check the quali...
Link to promoter database
epd.epfl.ch//i...
List of transcription factor binding site prediction tools
PROMO alggen.lsi.upc...
Transfac genexplain.com...
TFBIND tfbind.hgc.jp
CiiiDER bio.tools/CiiiDER
JASPAR jaspar.genereg...
ConTra bioit2.irc.ugen...
MORPHEUS biodev.cea.fr/m...
PlantPAN plantpan.itps.n...
PhysBinder bioit.dmbr.uge...
LASAGNA biogrid-lasagn...
MatInspector www.genomatix.d...
Transcription Factor Matrices bioinfo.lifl.f...
AliBaba gene-regulation...
MatrixCatch gene-regulation...
AnimalTFDB bioinfo.life.hu...
Tfsitescan www.ifti.org/cg...
TRAP www.ifti.org/cg...
rVista rvista.dcode.org
PASTAA trap.molgen.mpg...
DiRE dire.dcode.org

[@kumaribhavya10]

Hello, I found your video so useful, as you have enlisted so many tools to identify the transcription factor binding sites in promoter. I have one question let's say I have a transcription factor and just wanted to know my X transcription factor bind to on which promoter site of the gene, but I don't know how to do it. I feel I have to find the first gene or protein where x TF is going to bind isn't it? But I am just looking for your inputs in this. Thank you:)

[@nrttaye4033]

Hello, I am glad you found it useful and thanks for the question. I quite agree with you on that. There are also tools available where the set of genes can be identified for a particular transcription factor. Here are some of the tools 1) Gene Set Enrichment Analysis (www.gsea-msigdb.org/gsea/index.jsp) and 2) Harmonizome (maayanlab.cloud/Harmonizome/). These tools let the user input any transcription factor and displays the set of genes regulated. Let me know what you think about this.

[@bhavyathakur5361]

@@nrttaye4033 Thank you so much! I will try this tool and sure I will share my experience.

[@nilanjanaghosh8288]

Hello, this video is very informative. Is there any specific reason for choosing the start of the gene sequence to -2000? Or it could be changed according to the need?

[@nrttaye4033]

Hello, thanks for reaching out. The identification of DNA sequences that are biologically relevant TFBS is challenging. The promoter region, located a few hundred base pairs upstream of the TSS, is a hotspot for TFBS. It frequently houses critical regulatory elements such as the TATA box, CAAT box, and GC-rich regions. TFBS can also be located further from the TSS, in enhancers, silencers, and other regulatory areas. The chromatin structure and 3D arrangement of DNA can also influence TF binding. Some TFs bind to locations far from the TSS but brought into close proximity by chromatin looping. Thus, to answer to your question, you can definitely change according to the biological questions being asked.

[@nilanjanaghosh8288]

@@nrttaye4033 Thankyou so much for the reply. I understood what you explained.

[@narbahadurkatwal7154]

Hi, your video tutorial is great. However, I did not find my target gene's binding site (in the promoter region) even though I follow your tutorial. They are only showing the specific genes promoter region, so is there any other way to identify the binding sites? I would appreciate for your help.

[@nrttaye4033]

hello thanks. if you own an educational/institutional email id then MatInspector can also be used to identify the transcription factor binding sites in promoter. The trial version is valid for 30 days i guess. all the best.